Yeah it is a stereotyp for lesbians. That is not wrong in any way. It does not mean all lesbians are like that or are not like that. It just means if a women acts like a tomboy people mostly assume this person is a lesbian for no reason whatsoever. If this is bad or good depens on the person on which it is assumed. I just wanted to point out, that every human being is different and it is wrong to just say those specific type of people are all this. Because they aren't in any way. I also don't like to just assume all human are hetero it is also plain wrong and dump to say that.
And there are people who just saying all uchi characters are lesbians because there are all tomboys, THAT especially is a bad stereotyp. Because not all lesbians are tomboys and there are lesbians who get offended by that pretty quickly (as you said before there are lesbians who identify as tomboys but there also not). This does not mean all tomboys are bad lesbians or are bad persons. Which is just false. It just means not all lesbian are tomboys. And not all women want to be associated with lesbians because there are tomboys.
How would you feel if you where a hetero girl and you have a short haircut and act tough and everyone is just like "Oh yeah she is a lesbian because she has short hair!" You would feel offended of it because in this case it is a stereotyp which is dump to assume your sexuality on.
In this case yes. There are just fictional characters in a video game. And they would never complain, because they don't have any programmed genders or sexualities. Still it has a bit of salt to it. Because especially people in the LGBTQ+ Community should now such things are not matter out of there experience.