I received this clarification from Corey today on Collateral damage. Seems there will be no shenanigans with collateral damage canceling bunker and whatnot.
"I can see how my answer was not very clear.
My original intention is that Collateral damage happens AFTER all
skirmishes. I previously answered this the other way around, but have
decided that after all skirmishes is best.
I apologize for the confusion.
-Corey Konieczka
Fantasy Flight Games
Design and Development"