General Table Talk

Which, as I said, may work more or less for flaming swords, but not for MutoForm spells. If you allow a grog under Eyes of the Cat to still strike despite this, you're doing intelligent parma.

I'm sorry, I just don't understand what you mean.

Things that are fully magic => Does this mean Creo-ed things?
Things with magic that affect the one with MR => ??? You mean things that have non-creo effects on them and that are brought to the magus?

If so, your exemples are wrong.

The boulder exemple says that Mutoed items are resisted, not suppressed.
The flaming sword exemple says that the effect is suppressed, not resisted.

If you mean something else, I just don't understand what

It depends whether there are active effects or not on the talisman. If there is, can they penetrate?

The Aegis having to penetrate could have provided a partial solution. Alas...
So no, I'd say it doesn't...

Unless we rule that the Aegis doesn't affect magical effects that are under a Parma. Which could make sense.
OR

Unless we rule that Aegis/Parma/MR don't affect constant effects.

Which would solve this problem, and mean that a sword enchanted with a constant (sun duration, 2 uses/day, +3 constant) Edge of the Razor of Flaming Blade would not be resisted. Saying, in short, that constant effects are natural.
Which should work, mostly, as far as I see it. This changes the setting, though, making permanently enchanted weapons valuable and useful against both magi and magical creatures.
It also means that if you go through fire created by a constant effect, you get burned.

I seem to recall David Chart saying they used the RAW MR because, through numerous playtests, it was the one with the less bugs and problems.