Dude, I had this exact same question. Technically, the GUND-Format allows a pilot to connect with the Mobile Suit, or Gundam, to the point is possible for it to have some direct control of it using the mind. The only caviat is that, the permet system inside the MS will treat your brain as part of the system, and as result, will flow all the data of it inside your brain, fucking it up.
But if you were to survive that shit, all your "data", Aka, soul?, consciousness, will get absorbed by the machine, as now you are treated as part of the permet system inside it.
Honestly, you could developt a real Sentient AI by using the GUND-format without the need to fuck up the pilot...kinda like a copy of consciousness.
This AU had so much fucking potential to do and explore so many things, what a waste.