edit: Bringing this back since Netflix has EVA now
(Disclaimer: I have never seen Evangelion and picked most of this from fanfiction writing prompt threads, cultural osmosis, and wiki binging)
While the soul of unit 04 is unknown, the fact the unit is referred to by Kaworu as male in videogames, and that it had had Kensuke as a pilot in some of the alternate timelines brings up questions/ fan-fiction possibilities.
While both haven’t occured in the same spinoff, this opens the possibility that if the same soul (or the pieces successfully extracted) is put into 04 in each timeline, and the standard procedure is to use the soul of the pilots biological mother, then this could be the first Trans-male EVA, powered by someone closeted in life.
Given how little is known about unit 04,
the exact gender identity of the soul donor would be an exercise to fanfic writers.
Of course, Rei almost certainly didn’t have a biological mother’s soul in her unit, but given the series if Kensuke had a decent synchronization rate it might support the theory of the soul being from a biological relative.
Course with multiple writers and the possibility of different souls being used in different timelines, I suppose a soul taken from a random man could have been used and inserted in the timeline where Kaworu pilots it if SEELE decided Kaworus’ nonhuman ability to synchronize however they desire would would make the identity of the soul irrelevant.
Either way, this is a launching point for not major event changing stories, but opportunity for fanfiction to fill in blanks.
Monsters and Stuff 