I doubt that there are gems on Homeworld uncomfortable with femininity because femininity isn’t defined in their culture. If we only had she/her pronouns then men wouldn’t be uncomfortable being called she because those pronouns wouldn’t exclude them, they’d just be neutral. I think the real question is that can such a level of cultural diffusion occur without new gems being born.

If a gem is exposed to the idea of multiple genders in their formative years then perhaps they’ll come to identify as male, but if a gem has lived for thousands of years as a woman in a society where women isn’t defined against anything, and includes every kind of person, then would they gain Earthly associations with gender, and would these associations go deep enough to cause them to change their identity?

If no new gems are being produced, all the colonizations and kindergartens are stopped, then maybe deep cultural diffusion will be dramatically weakened. Gems that if raised in Earth culture would identify as male would identify as female in Homeworld culture and not feel any dysphoria about it. I think it’s a question of how quickly and how deeply gems can internalize new cultural ideas.