Oh yeah, Japan is a bit weird that way, or it might be more accurate to say that the west is weird.
The anti-gay sentiment you see in conservatives in the west largely stems from Judeo-Christian doctrine.
In Japan, Abrahamic religions are in the extreme minority so oftentimes homosexuality isn’t seen as a sin but rather just something that differs from the norm.
However, Japanese society is also more intolerant to differences, so instead homosexuality ends up in this weird grey area where it’s used mostly for drama or humor in the media, but in real life it’s very much a case of “don’t ask, don’t tell”