Gaynst in manga used to be very common. But then, manga was the only place you would ever read anything gay anywhere outside of spec-scifi stories and at best you would get a bittersweet ending. Because that is what reality was like, you were barely accepted by anyone, and in Japan, it was treated as something you grew out of for girls and something you never reveal to anyone for boys.
Now that more places are more accepting, these stories remind us that Japan hasn't really progressed much IRL about Queer issues with
Gay Marriage being shot down every time it has come up. But with the younger generations now being the ones writing manga, there is more hope in manga now with happier endings being commonplace even if it isn't exactly true to life.
With how accepting the mom is, the son could come out to her, but since they are in Japan, he is very wary of doing so, especially since he is still in school. Conforming is a pretty big pillar of morality in Japan and being disowned is a very real fear he would have.
If this is really the end of the manga, it feels natural given the subject matter and tone. Maybe in the future we wouldn't have to worry anymore but sadly, it seems like we are a long way away from that being a reality.