Mutant Genesis: In a similar vein, if I play Mutant Protectors and the boost card’s boost effect defeats the ally that was…

Yes. Per the rules of Defense-traited cards, the identity that plays them becomes “the defender” for that attack. Mutant Protectors is just a special case where being “the defender” is immediately passed onto the X-Men ally put into play. Should that ally leave play due to a boost effect, we are ruling that the player that played Mutant Protectors (a Defense-traited event) would revert to being “the defender” in that situation.

-Alex