Note that we are talking about house rules here anyway.
When ArM5 basic rules stood alone, there was no reason at all to have Aegis and Skinchanger interact.
At that time we recommended to new players the "Flambeau Spitfire": get an eagle or raven shape via Skinchanger for one Virtue point, Deft Ignem for another, lots of Ignem and magical combat for the rest, and then fly in and 'let fly'. it was cheesy already then, but it was legal. (OK, "Spitfires" walked around butt-naked a lot during adventures, and that gave the rest of the troupe a lot of "role playing opportunities".
)
With HoH:MC out some time later, the "Spitfire" turned from cheesy to fishy (and was no longer recommended), as the commitments and downsides of the Bjornaer became apparent. I recall a lot of resentment then about the new perspective of House Bjornaer wrt Hermetic shape changing. And also Bjornaer Heartbeast skill was no longer all benefit compared to the one Virtue point Skinchanger: some Heartbeast skill was indeed needed to change under a foreign Aegis. But still the Aegis and the Skinchanger had no reason yet to interact.
With HMRE out some time later again, that changed. The question arose, how a Skinchanger prepared his new magical animal skin, if his old one got destroyed. We knew that it took "a season, although the method varies depending on what the item is." Well, that is quite what we knew about the Folk Witch's Skin Nitting (HMRE p. 40), too: "If she has the Shapeshifter Ability, the folk with may enchant an animal skin in her kitchen. ... enchanting the fetish takes a season and consumes 1 pawn of Animal vis." Also, the procedure with which a Skinchanger prepares his skin is accessible even to illiterate grogs and does need time, but neither lab nor vis. All this fits with Skinchanger being a 'low tech' version of Folk Witch Shapeshifter, even doing away with the Shapeshifter ability - which helped to bring Skinchanger in line again with the rest of the shapeshifting, as that had developed over some four years after the ArM5 basic rules were published.
And as already the Folk Witch's Shapeshifting is by HMRE p. 7 very much hampered by the Aegis, the Skinchanger is affected by it even more severely. ...
Note again, that we are talking about house rules here. House rules need to respect already established character rights and histories. If a campaign contains a "Spitfire" or such, which already has decided Wizard's Wars or Marches with its ability to sneak in animal form under the Aegis and kill the target/nemesis/villain, you can't take that away by introducing above house rule.
But with over two dozen ArM5 books at hand now, I don't believe that Skinchanger can just remain the simple no interaction required, no strings attached, no explanation given power that it was when the ArM5 basic book came out 2004.
Cheers