Yeah I feel the same way.
I always lose the perk like a week or two in a new game and it feels like wasted potential, like instead of just losing your male identity immediately it would be interesting if there were levels to the male origin perk, like at the start of a new game with male origin your character will gain more confidence/happiness from being physically strong and winning fights and could be against wearing "girly" clothes, and could have interactions with both male and female characters where they forget that they are, at least on the outside a women before becoming more comfortable with there new identity... or not... maybe you character will refuse to accept their new body and will do anything to get there "true" self back no matter the price.
This could also be a cool way to add a origin where your character was trans before the start of the game or maybe they never realized that they didn't truly identify as a man until now and feel more comfortable in this new body, but there all the more vulnerable in this new would.