I don't know about Crystal, but yeah in the original dub they tried to censor it by saying Haruka and Michiru were "cousins", but didn't do anything about the subtext.
^ Yeah but that's a whole different to have the transgender flag and the character being transgender. I believe i saw on Reddit that's because the artist headcanon Aoi has transgender but i have found no real proof of that. Also mentioning that people think Aoi being trasngender is valid headcanon of the description of the show saying that Mira thought Aoi was a boy when she was younger. I have nothing against transgender and actual transgender representation is low so i'm ok that people headcanon some characters as such but saying it's valid only base on a bad assumption of a kid it's a bit farfetch.