the girl models and the boy models are slightly different. you can see the difference if you find the rip of their models. male model is slightly taller, female model has larger hips. they also have slightly different walk animations.
if male clothes were enabled for female models and vice versa, the clothing models would have to be retooled to match the models and character animations.
usually when studios make decisions they look at how many development hours they would have to put in to a feature vs. what percentage of their users will use it. this is why games often have better animation, more cutscenes etc in the first half of the game vs. the last half, because statistically most people don't finish longer games.
when it comes to crossdressing, such a small percentage of players would use it that it's probably just not worth it.
honestly. if you look at percentages of player stats on how many players play male characters vs female, it's usually overwhelming male. pokemon might be different because its fanbase is about 50/50. but even though people think of the male dominance of video game characters as a cultural thing, it's probably mostly a development hour calculation.
sorry for the rant just took my adderol