C - Really? That's what you get that from my stoneskin analogy? That an effect that goes around hurting a lot of magi in your saga?
If you really don't see a diff between your example and mine, I'm hesitant to try to explain it, but I'll give it one shot.
I don't see why you selected a direct-damage spell with duration as your (absolutely spurious) counter-example - that's no different than any other fire-based attack spell. A direct-damage spell with a duration needs to penetrate once it comes in contact with something with MR, same as any direct damage spell. Pilum of Fire doesn't have a Target of "that guy with 500 MR" - it has a Target of "Individual Amount of +15 damage Fire". Doesn't matter if the effect is carried to the MR, or the MR walks into the duration effect - the magic needs to penetrate the MR to damage the hopefully-soon-to-be burn victim.
A ward is different because it's not trying to penetrate anything - it doesn't need to affect the MR nor the thing with MR. No effect is trying to be placed through that MR, no damage is trying to get through - the effect is already where it wants to be, guarding the original Target. The Ward stops (or tries to stop) the thing MR'd, or (in the case of Aegis) reduces any effect from that creature.
There is no rationale as to why it needs to penetrate except that "other spells need to penetrate" - but these don't work like "other spells", not even a little bit. So much so, in fact, that they have their own little subsection of the rules to make that clear. And there is nothing - nothing in that section about "penetration".
"Rego spells can create wards which protect the target from things of the appropriate Form... the target is the thing protected, rather than the things warded against... Warded things cannot act across the circle..."
There is no "unless they penetrate", nothing of any sort. Not sure how much clearer that needs to be. Blindly applying outside rules like a blanket, even otherwise "universal" rules that directly contradict the above statements seems completely out of place to me.