If a blinded pilot card (from the new deck) is assigned to a TIE Phantom that remains cloaked during the combat phase, does it count as an opportunity to attack for the purpose of flipping the card? Logically it shouldn't, since a cloaked ship cannot perform any attacks but I've seen some very unintuitive rules in this game so I'd like to make sure.

No, it doesn't count because the Phantom didn't have an opportunity to attack (as it was cloaked).