Maybe a bit of a stretch, but I might consider the first NieR for this list. Exactly half of your party in that game is explicitly queer and while it is plot-wise largely tertiary information, there is some very pointed word choice in the dynamic between the two queer characters that leads me to the conclusion that it runs pretty deep into that game's soul in a way that is so loving as to be genuinely shocking from the presumably cishet and "sort-of-weirdo judging by Automata's character designs" Yoko Taro.