This is a good discussion. I myself was thinking of my magus enchanting a sword as a talisman, even though I intended to design effects that can be switched on or off (I'll ignite it by spell if I want Penetration. But I was told just opening it for enchantment made it resistable. This confused me but I went with it, reasoning that a talisman shield would prevent those with MR from even touching me.
These are still future projects.
In games I run, I use the common HR saying MR blocks the effect, not the item, so far ranging implications such as this never occured to me.
So, if I enchant my sword or shield as a Talisman, I cannot even pick it up because of my MR. You can say it is an extension of me or I let it into my parma. Fine.
But what vof the classic story of discovering the talisman of some long gone magus, or stealing one from a living magus? Just being enchanted means I cannot pick it up. Cannot study it in the lab. Nothing.
Maybe I'll just stick with spellcasting.
The fairly simple rule I like to use is:
if you could invent/invest the effect with penetration, then it must have penetration. If you cannot (opening an item does not have rules to provide penetration) then it's not classed as an ongoing magical effect and as such does not interact with the MR/penetration rules.
Thus, a sword that is opened for magical enchantment but has no effects in it gets treated like a sword. If you stick it in someone with magic resistance, they will get a sword-shaped hole in them unless they have some other defense (ward against swords, greater immunity: swords, a shield, the ability to get out of the way, etc).
The alternative is the scenario of a magus potentially not being able to use their own magic wands because of their Parma. And that's just silly.
I like magic weapons so my current Scions of Nathas saga has a boatload of them, some of which are scary powerful.
I handle magic resistance by saying that MR protects you from the effects of magic and thats all. It would stop a magically conjured sword. It would stop the fire effect on a flaming sword from hurting you. It won't stop the sword itself from cutting you.
Assume your basic standard flamey sword. i.e. a lesser item enchanted into a sword to make flames wreath the blade to do more damage. If you try to run a magus through with it, his MR might stop the flames but won't stop the sword. He'd need a terram ward against that.
Of course this gets rid of the pink dot problem entirely while introducing other issues. But i've found it works so far. And it lets my players have cool enchanted weapons that work on anything, even if the magical effects in them do not.
Not that I'm picking holes (I'm not, it looks workable) but under this system, what happens if I turn a boat into an arrow and loose it at my MR-protected opponent? Have I just successfully hit him with a high-velocity boat?
Yup, one of the main "suppresses magic but item is unaffected" problems is that. We had that discussion with a boulder-throwing sling in my group. We have also played around with "parma acts at reach range and above only" (touch range or less unaffected by parma; shields Dune style), but that has problems with the magicians that go for the close combat approach, even if we prohibited precision teleporting to avoid magical assassins jumping stabbing and moving away.
The final thing is: as long as it works in your saga, it is amazingly cool, whatever it is 
My take on it, and I'll admit this is a little fuzzy (but this is magic so sometimes it's a little fuzzy) is that magic resistance protects you from magic which effects you. The fire on a fiery sword is magical and effects you, so magic resistance would protect you from the fire, but not from the blade of the sword. A boat turned into an arrow would strike as an arrow... the magic doesn't effect you, it effects the boat/arrow... so you don't resist it. Likewise, if I did a muto aquam spell to turn water into acid, the acid would burn you because the magic isn't effecting you, it's effecting the water. The changed water isn't magical.
You had me until the muto water into acid...
Why?
Probably because the "acidic" property of the water comes exclusively from magic. It should be resisted, IMHO.
I throw a bunch of Sand at you and fast cast a spell (turn sand grains into boulders) that I have mastered for that cause. Rain of boulders on you. I would have problems seeing a covenant survive this single spell. Similar spells are easy to design that are bound to be easier using easier to affect forms.
Xavi
By RAW, magic resistance protects you.
That same boulder would bounce on the Aegis.
I know, but not by Mark's rules
So magic that causes an item to do less damage (boat to arrow) is ok but magic that causes an item to do more damage (water to acid) is bad?
What about filling a glass with poison and turning it into wine. Is that "not deadly" property of the poison/wine resisted?
Yup, except of course that the boulders will hit each other first, boulders being much bigger than grains of sand... and also much heavier, so they probably wouldn't go as far. Of course, I could turn the air around you into fire... or lightning, which would still be auram and not even need a requisite, and fry you. I could turn the earth under your feet to quicksand, or just open a huge hole under you and then drop the sides down on top of you. Sure, there are tons of ways to alter someones environment in an effort to kill them while bypassing "direct-effect" magic resistance. There are only slightly fewer ways to bypass RAW magic resistance if you're clever.
To my thinking, magic resistance ought not be the "end-all be-all defense." Magic resistance ought to useful, handy, even cool... but why should it be battleship armor with a side order of force field and a cherry on top? Why should magic resistance protect you from every imaginable magical attack?
It is simply more logical, to my point of view, to suppose that magic resistance protects you from being directly effected by magic. That sets up some very neat and clear guidelines and avoids questions like the original poster's, who wondered what to do when a magus's talisman sword struck a magic resistant critter. If magic resistance only prevents direct effects, the matter is clear... does the magic effect the critter? No. Then the sword hit's home. Neat, simple, easy. Does it have different rules implications? Sure. But I don't think they are any crazier than the whole pink dot mess.
Old debate. Per RAW, you can't drink the transformed poison unless it penetrates. Per a house rule, well, that depends on the house rule.
The original poster's inquiry was about RAW, I believe, so this whole discussion has drifted off-subject.
A simple answer to his question would be that providing an enchanted object with penetration for its physical properties could simply be a ReVi effect, 2 points per level. It does not affect any of its other powers, which must purchase penetration seperately.
So, for example, you have an enchanted sword as your talisman. You want to avoid it bouncing off magic resistance, so you invest it with a level 30 ReVi effect that provides the physical sword with +60 penetration. You later invest it with Blade of the Virulent Flame, for which you purchase +20 penetration by adding 10 levels to the effect.
You attack a magical creature with MR 30 with your sword. The sword itself penetrates, but not the virulent flame. You do normal sword damage.
Don't blame this on me!
I am just theorizing. Previously in my saga we used RAW, but a non-penetrating condition (such as being attuned or taking a longevity potion) did not make something resistible.
The way I look at is that a Mutod object has part of its essential nature overwritten with magic for the duration so the object is as much a magical effect as one Creod out of nothing and so it cannot pass through parma unless that muto effect has enough penetration.
W.r.t magic swords: The image of a thing is not the thing itself which is why Wizard's Sidestep can be a Re effect rather than Mu. Therefore the pink dot trick will make it look as though the sword has been stopped at the parma but the wizard still gets chopped. The flaming sword likewise gets to cut but must leave the flames at the door. There are subtleties however, if the flames have heated the sword blade (which they would do unless the effect is designed otherwise perhaps to avoid damaging the temper and/or protect the wielder) then the blade will be burning hot when it strikes if, on the other hand, the effect is a range personal CrIg that heats the blade directly then the blade is suffused with a magical effect (the Cr'd heat) and bounces.
Edit: Actually that last line is problematic because the sword heated by an ongoing CrIg is analogous to a person with an ongoing CrCo healing or longevity effect and having magi bounce off each other gets silly. I guess I'd have to rule that the sword does cut but the heat does not affect the resistant creature.