Pluto, Luna-Terra and Mercury are very heavily implied to be trans. It's a more prevalent theme in Luna-Terra's route than it is in the other two, but she does have a conversation or two with Pluto about it, and it plays a big part in Pluto's guilt over being allowed to be anything, but not knowing what to do with it. As for Mercury, there's a mail in Saturn's route in which he has an argument with (I think) a medical examiner, over hormonal therapy.

It's never explicitly spelled out, due to in part being a game intended for an audience that is already familiar with these sorts of things, but most importantly one that thinks it's funny to use exposition as a tool to confuse the reader even more (which it is). Missing things on a first read is completely understandable, even for a native speaker.

Thank you so much for the answer! It really helps me a lot.

It's not merely "implied", it's as explicitly stated as it can be.
There are direct references to hormone therapy, deadnames, and other aspects of transitioning.

Spoilering just in case anyone wants to discover the details in-game for themselves:
Pluto and Luna-Terra are trans women. Mercury is a trans man.

Even Saturn's relationship to gender - despite her being ostensibly cisgender - stands out, in that she's the one most invested in transhumanism; in becoming something other than human, something truly alien.

Aevee Bee - the writer - is a trans woman herself.