Both spells take effect they don't cancel one another. It would be as if two characters are wrestling over the stone with naturally somewhat more control exerted by the stronger spell.
So are Casting Totals compared or an opposed Finesse Roll to determine who gains control , or is it round by round?
Since those are Concentration duration, should it be resolved as Int + Concentration (Int + Finesse for other durations)? Should there be a bonus for spell magnitude or casting total?
Since Ominous is a 2-round spell, I can see a slow Unseen Porter stopping the stone from dropping. But can you take control of an incoming Crystal Dart with a fast-cast Unseen Porter?
It's more the mechanics side that I'm looking for opinions.
Nice! In the suggested case we would use casting totals compared. We would include penetration in the total. If you lost "a round of combat" you could cast the spell again to see if you did beat the casting total of the other magus and gain control of the stone. If your spell was stronger, you get it. If your spell is active when the other expires, you take control as well.
The important thing is that this is a dynamic contest where the casting totals are known. You do not need to have the casting total of every single spell with a long duration written somewhere. That would be annoying. Having a casting total contest is not problematic in a dynamic combat-like situation, though. It is just opposed rolls in the same scene.
Cheers,
Xavi
Initiative tells you which one goes first and which one goes second --- so in some contexts that might be significant. For example, if two Leaps of Homecoming sort of spells are cast on a target at once, then the first has its effect and the other one is too late (the target is no longer available). Or if the first spell, say, moves objects to break a ward, then the second spell will move the objects away from the ward border, but that will be too late; the ward is already broken.
Otherwise, (or if Initiative totals are equal) then both spells are active. If their effects act to cancel each other out, then that is exactly what happens, their effects cancel each other out. This situation persists until either one of the spells expires (which might be due to failed Concentration roll, if Concentration is its duration) or is dispelled. If one spell is still active, when the other expires, then the still active spell is indeed still active and has its normal effect, until it too expires.
You don't need to compare Casting Totals or Penetration (except for the usual reasons). There is no need to make up rules, the existing rules work satisfactory.
You might, depending on context, want to check the magnitude of the guideline the spells are based on (if they are based on different guidelines) to check if one spell really does cancel another. For example, a spell based on the level 1 CrIg make light guideline, probably wouldn't be sufficient to totally cancel out a darkness created by the level 2 PeIg guideline. However, it would probably act to "lessen" the darkness somewhat. Both spells would still be active (until their respective durations expired) so if the PeIg spell expired, then the CrIg spell would have its full effect, until it too expires.
So you cannot wrest control and have to wait for a Concentration roll failure. Ok.
And what about Unseen Porter as a fast-cast defence to Crystal Dart?
I think by RAW multiple spells affecting the same target affect it at the same time, as long as their durations overlap. RAW doesn't say what happens when they now contradict. In simple cases, such as "spell A provides -1 and spell B provides +1", it is plain to see that they cancel out. In cases such as fighting over the stone or whether the target appears like a pig or a human it isn't clear what to do by RAW.
I do not think it is RAW that spell B takes affect instead of spell A just because it is cast later. Both spells still affect the target, they both penetrated and still have an ongoing duration.
I don't think there is a RAW solution. I liked the idea of comparing the two spell's base levels, although that still leaves us with the problem of what to do with identical base levels. I'm tempted to say that in the stone's case it will drift in the direction that isn't canceled out, but that's employing modern vector analysis.
Reverting back to my previous suggestion, I'd say that when the two base levels are identical and the spell is cast with as much "force" as possible, you should compare the Penetration of the two spells. This is a nice measure as it means that generally the stronger wizard would win yet doesn't count the power spent on increased range, duration, or target. If the problem is that you don't have the Penetration of the previous spell - just estimate it.
This works, and is certainly preferable to not having a basis for which takes precedence.
While in general I would certainly use base levels and penetration totals as you suggest and I agree that this is a matter undefined in the rules as written, in the specific case of transformation spells however I think that you're making a poor choice.
You're adding complication where none is needed, if you've ever seen new players shut down because their target individual corpus spells don't work on giants you'll be hesitant to add more things that can screw up a new player or even a fairly experienced one.
I think adding a layer of possible argument regarding whether or not two transformation spells contradict one another is a mistake from the perspective of the game running smoothly. Here's an example if a spell that turns an animal into a human is a counter for curse of circe then how about a spell that gives the pig a set of human arms it rather defeats the purpose of the spell, if not a spell that gives the pig human arms how about a spell that changes the pigs limbs into human limbs, and if not that one then how about one that changes the pig's head to make a pig centaur. I'm not saying you couldn't draw a line, I'm saying you couldn't draw one that wouldn't lead to confusion and argument among at least my players.
I also think that it is a mistake from an internal consistency standpoint the spells say "transforms target into..." a rule of thumb that works very well in the game is that if a spell is cast successfully and penetrates it works. That isn't just a system issue it's an aspect of the setting that comes from the system and your ruling would compromise it.
The other conflicts between spells such as fighting over a rock happen precisely because both spells work. The case of transformations is different because you're saying that one of the spells doesn't.
We should use the RAW and ask is it a valid target? Did the spell get cast successfully? did it penetrate? if the answers for these questions are al yes then the spell worked. It's complicated enough already.
In a way, you are saying magic is a continuous push that stops once the spell is over. The opposite view is that magic is flipping a switch that will reset after some time.
This does not work. Turning a man into a sheep for a month then turning that frog to human for a day, should the first spell push back into sheep in an instant? Spell A gives -1 then spell B gives +1, should the result be -1 because A is stronger? Should 2 widely different spells with a minor overlap be mutually exclusive?
No, the man will be himself for a day, and the bonus should cancel out. If you want to model the fact that a spell is resistant to override, add a magnitude for some ReVi requisite. Or make an unlimited use item that maintains concentration.
I think some ruling needs to be made, if this comes up, since it isn't addressed by RAW. I agree that your ruling is simpler to apply and doesn't produce exceptions to how a spell works - if it is cast successfully, on an applicable target, and penetrates, then it works. However, I don't like the fact that it can render powerful spells irrelevant. This isn't just about transformation spells - what about a ReMe spell to make one happy, and another to make one sad? Or an InMe spell to bring a memory to the surface versus a PeMe spell to suppress it? A PeIg spell to snuff out the light of a CrIg spell? Some general "Magic Theory" needs to be established on how spells function when they work against each other, and your suggestion of "last spell wins" I think trivializes ongoing effects.
I'd point out that spell A is trying to assert the Platonic-Form of a "Pig", and giving the pig human hands or so on hence works against it. In contrast, maiming the pig doesn't (it's still a pig - just a maimed pig), nor does killing it (it's still a dead pig), or so on. Yes, this can still lead to arguments - but then, so can many other rules and rulings.
The whole point is to make a ruling about when two spells can't work together. Everyone agrees that spells usually all work. The problem is not with transformations per se: your can MuCo yourself to have eyes of the cat and lungs of the fish at the same time, and you cannot ReTe a stone to both stand still and move at the same time. So the question is, what to do in the cases where the spells on a target can't all work at the same time?
I agree your way is simpler. I don't like just letting the last guy win, however. My way, there is the possibility of intentionally using a high base to strengthen a curse, and a weakling magus cannot easily undo a powerful spell (using a lower guideline). I feel the complexity can lead to greater story potential, and that makes it well worth it.
I don't think that second view is RAW. It is contradicted e.g. by Suppressing the Wizard's Handiwork, the way wounds only heal once the duration ends, the way area spells keep affecting new things entering the area, and so on.
Why? Where does RAW indicate this?
As far as I can tell, RAW says that multiple spells all work simultaneously, and doesn't say what to do when two such spells cannot be imagined to work together. Handling such cases hence requires house rules, and this is where considerations such as ease and consistency of play and in-game effects come to the fore.
I don't need to add concentration for the spell to keep asserting itself. It just keeps on working. And I don't need to add requisites to house rule that some spells are more resistant to overrides than others - nor need you add anything to house rule that they aren't.
Make the effect of a spell have a magic resistance of 5base level or 3base level if you do not know its penetration total. If you contradict the spell effect (move an immobile item, or turn a transformed human back into himself) you need to beat that effect.
Easy plug solution.
Xavi
With some of the discussion recently on essential nature , some questions.
Why would the harvested wool and cheese (milk) not instantly revert to the unviolated by muto essential nature of the squirrel?
It isnt the same process as that for Creo (page 77) , whereby a magically created horse eating mundane food leaves mundane dung.
The spell only affects the squirrel , as soon as any part of it is a separate individual thing , the muto spell no longer affects it.
So shorn wool becomes squirrel fur and if you can get squirrel milk , it should make an interesting exotic cheese.
The Muto spell violates the original essential nature , as long as it is maintained , but does not make permanent copies of the imposed nature.
They would revert after the duration. The Muto spell would need to be cast on the Wool/Cheese or it would revert after the duration of the spell on the squirrel in effect when the cheese/wool was harvested expires.
Creo magically creates a mundane horse... So mundane food in, mundane Poo out.
What i dont get is how Muto spells fragment in this manner or it is accepted that they do.
The original spell was say target: individual or target: group.
People keep talking about trees bearing fruit or animals getting pregnant.
Once the fruit is picked or the animal gives birth , it is a separate individual ,
not covered by the original spell target.
So it should revert to whatever the target of the spell originally was , immediately.
Not when the duration of the individual spell expires.
Same with wool or milk/cheese in this case.
I use sufficiently high level Muto Vim with requisites to turn a spell into an apple.
Remove seeds , use CrHe to quickly grow to maturity & ReHe to get fruit immediately.
Pick the fruit. Do i have fruit as long as the original spell is in effect?
Does it revert to being copies of the original spell?
Or does it simply become a burst of magical energy that could give you warping points?
Hmm.... So you are saying that if I cut the paw of a shapeshifter wolf it reverts to be a human hand immediately? Certainly not how we play it around here...
Xavi
Nope , that is not what i'm saying.
The paw is part of the original target and when you say shapeshifter ,
do you mean human changed with ongoing MuCo spell into a wolf?
Because i was not referring to the Shapeshifter Virtue at all.
Mystery Cults for House Bjornaer (page 22 , Ringing the Changes) covers the various shapeshifting options.
And the Our Saga Does Vary goes without saying for certain Iberian Campaigns. 
Manx campaign right now 
In this case it is a thing of "we never thought about it" more than anything. I am curiosu about the reasoning.
Cheers,
Xavi
My reasoning (current obsession anyway) is that a Muto spell affects a particular target , say Individual.
While the spell has duration all of the original individual is covered by the spell.
Even if you sever bits.
If you shear a squirrel turned sheep , the first fleece you get is part of the original target and stays as wool ,
until the duration expires.
Any subsequent fleece , grown naturally or by Rego is not part of the original target
and as soon as it is separate from the original , it reverts to squirrel fur.
Any dung produced after the first crap it has , will also revert to squirrel fewmets.
Unless the squirrel was pregnant at the initial change , any pregnancy after the change ,
results in baby lambs reverting to baby squirrels as soon as they are born
and no longer part of the transformed mother.
An essential nature can be violated by a Muto spell
but you cannot create permanent copies of the imposed nature.
Shearing a transformed squirrel as sheep for multiple fleeces for example.
It works exactly the same the magical horse creates mundane dung, the magical cow creates mundane milk (and mundane dung).
Edit: I see the conversation has moved on.
My take on Ravenscroft's model where the cow would produce squirrel poop rather than cow poop, is that I imagine that it would be a tough idea to get across to players and would rob their characters of cool things that they can do and it wouldn't solve any real problems in the game (if your magi characters can't generate wealth they're not trying hard enough