This is for the best. I understand the argument of "oh those scenes recontextualizes his internal homophobia", but that only works when the romance route is in the game. If not, then you get scenes that reduce Kanji into a joke rather than strengthen the game's themes
I do not care about Yosuke's homophobia being removed and the reason why is because the game never cared either.
It was always just there as a joke to mock (mainly) Kanji and it wasn't that funny.