(1) Certainly not an interaction with his disguise script: the disguise script changes his clothes by running UnequipAllItems and then EquipItem on all new outfit parts. THough, if an actor is in power armor, running UnequipAllItems will strip him of all power armor parts - and for this reason, the disguise routine has been blocked entirely if he's in power armor as of UFO4P 2.0.1. In other words: if he's still wearing his power armor parts after a location change, his disguise swap routine has not been running.
(2) If you say " ... BUT his PA helmet will be removed [...]", what do you mean exactly ? In the unmodded base game, followers are never wearing their power armor helmets (Paladin Danse is the only exception). If they do in your game, this must be the result of some mod - and I'd wager the guess that the missing head is a result of that mod too (the base game has no reason to disable his head, but if you want him to display his helmet, you MUST disable it).
It appears that actors are now wearing the PA helmet (when the game was just released, I've never seen them doing it) or maybe, it is still not lasting and they'll remove it on the next occasion.
Anyway, it still doesn't have anything to do with the diguise swap since that would have unequipped all power armor parts at once.