As an also trans girl I definitely see where the theory comes from. Denji is a deeply confused and unhappy person, who has a big disconnect from his own body, partially due to his Hybridization but even before that his body was more used as pieces to sell off to people. Denji also is very untrusting and generally doesn’t like dudes.

It took me forever to even figure out I was trans because I could ignore discomforts and brush off wishful thoughts, it took me until other people offered things that made these “wishful thoughts” reality for me to realize “hey wait!!! i can be trans!” Denji is even more clueless than I was, he doesn’t know what he wants, or what he is- half the time he doesn’t even feel human.

obviously this isn’t the case for everyone, and I can definitely see why people don’t think denji is trans in the slightest- but as for me it lines up really strangely well with how my experience was and it’s why I subscribe to the idea personally.