I can tell that your heart is in the right place, and you want to be kind and respectful to your friend. You're doing great about using their pronouns. I agree with everyone else's advice to not worry too much about it, though I know that it's easier to respect somebody different from you when things "make sense". Here are a couple things to think about.

>“if they see know they’re girly, and are okay with it, why does it bother them to be seen as a girl? They LOVE skirts and makeup, and strives for the same feminine beauty as I do?”

Could you imagine a man who likes skirts and makeup? Maybe a man who works at a beauty studio and always has his nails done, or a man headed out to a gay bar. What about a woman who likes manly things, like jeans and short hair?

>My first thoughts were something along the lines of “why would they chose to live a kind of life that makes then feel that way?”

I'm assuming you're a woman, since you say you also strive for feminine beauty. Sexism makes your life hard. Does complaining about sexism mean that you don't like being a woman? If you could snap your fingers and become a man, would you want to? Even if it would make your life easier?