If you have a working token or were part of the casting of the aegis, you do not need to penetrate it: the aegis does not affect you at all.
Xavi
Aegis of the Hearth (page 161)
This is for spells cast outside the Aegis.
If you are not casting a foreign spell , that is you participated in the Ritual , everything operates as normal.
It does not specifically address those with tokens leaving the Aegis and casting spells into it.
If the invitation is withdrawn , then the penalties apply.
If you cast another Aegis around an existing one ,
it must penetrate the magic resistance of that Aegis , to have an effect.
If you cast a Muto spell at someone already under the effects of a Muto spell ,
the new spell must still penetrate to have an effect.
The "magic resistance" of the existing spell is the Penetration Total of the Magus who cast it.
Page 22 in HoH:MC
Ah, I missed that qualifier "foreign". So it is explicit after all.
I recognize the difference between casting any old spell into the Aegis, and casting one that overrules it (potentially). However, I still don't think there's precedent to consider all spells as possessing MR equivalent to the Penetration when they were cast. The passage from HoH:MC is too specific and obscure to be convincing, IMO. It applies to shapeshifting but that's about it.
If spells do have MR by default, then (apart from the rather academic issue of doubling up Aegises) we get some interesting colloraries: for example, you can cast trivial high-penetration Muto spells on yourself or your grogs (such as turning them pink) and thus prevent the evil witch from Mutoing them into cockroaches (which aren't pink, so the pinkness spell will have to be penetrated). Cheap (though specific) Magic Resistance!
I don't think spells have any MR at all. Will Over Form is a special case. Only the PeVi guidelines have anything tangible to say about dispelling spells.
No, if somebody turns you into a newt and then somebody else turns you into a frog, there is no contest: you'll be a frog.
So any Muto spell cast on you , no matter how high a level ,
can be countered by any other Muto spell of any level ,
no matter how low that may be?
Base 10 : Change an Animal into a Human (page 118)
The Queen of Air and Darkness curses you with the form of a frog , say a Might 100 effect.
The pissy apprentice goes hey presto! with his level 15 spell and you are a human again.
Tell me how that works. 
Rego Vim Guidelines page 161
So in this case , only the level of the spell cast need be noted versus the level of the spell to be affected?
To cast the Rego Vim spell we only need a Casting Total to see if the spell works.
We can completely ignore any Penetration Bonus or subtraction of spell level from casting total as per page 82.
This general exception to the spell-casting process
only applies to any spell being cast on any other object or being that has a spell with a duration greater than Momentary in effect ,
except as noted in the special circumstances of using a Muto Vim spell on another spell that is being cast.
Please explain. 
If your spell outlasts her power, you're golden.
That's my opinion, yes.
I don't see what makes you think it is an "exception to the spell-casting process", nor where that notion that spells have MR comes from. If you want it as a house rule, have at it. But as things stand, the fact that your magus turned himself into a newt doesn't make it any harder for mine to turn him into a frog. So long as I breach your Parma, it'll work.
Vim spells take the target spell's level into account because in this case we aren't trying to work around the spell and affect the spell's target, but to affect the spell itself. That I turn you back into a man hasn't lifted the curse. A strong enough PeVi spell might.
Can you support this from the RAW though?
I can see nothing to indicate that any spell cast does not use the process on page 82.
You cast any spell in the book at any target , and you add Penetration Bonus and subtract spell level.
What spells are then exempt from this?
(we may need to start a new thread on this topic)
And I am not arguing that any does (except maybe Wizard's Communion 
). I just don't see where you got that a currently standing spell had a MR equal to its penetration to be used against other spells that try to subvert it.
If you have cast Eyes Of The Cat on yourself, and I want to cast Eyes Of The Mole, I need to penetrate your 5 x Parma + Form bonus, because it is you I am trying to affect. The casting total you obtained when casting Eyes of the Cat is completely irrelevant.
If you have left a Lamp Without Flame behind you and I want to MuIg it because I don't like its color, I only have to succeed in casting my spell - your spell doesn't have any MR in and of itself.
As for Vim spells, just as with fast-cast defenses, only the level of the spell you are trying to affect matters, not its casting total or penetration.
Is there any instance in which the Penetration total of a spell has any use whatsover after the spell has taken effect (or failed to take effect)? The principle seems to be that the Penetration total simply represents extra "energy" that is wasted and goes away unless used to penetrate MR.
I do have a vague recollection that there might be someplace that mentions the need to keep track of Penetration totals for later use, but I can't remember where.
Well, if you cast spells like Edge of the Razor or Shape of the Woodland Prowler, you want to keep track of the penetration to see if the spell's target can then physically affect someone who has MR. But I don't think it's needed anywhere else.
Which would leave us wondering why do Perdo Vim spells have to exceed at the least half of the targeted spells level to dispell it?
Form-specific dispels are easier than general dispels.