This question has spoilers for one of the endings of the Pallid Mask scenario. Be warned.

Through my actions the Man in the Pallid Mask got removed from the game...my understanding is that he sits out the remainder of the scenario in that case, but he goes back into his owner's deck afterwards, yes? I ask because story-wise he possibly could be dead/gone/done and I don't want to lug around an extra weakness if I don't need to.

A card that is "removed from the game" is still part of its owner's deck (you in this case), so you're not permanently rid of the Man in the Pallid Mask yet. Contrast with "exile" and "remove X from your deck".

That's what i figured.