Context matters. He only had these thoughts in relation to one guy, explicitly because hes aware he still has feelings on some level despite not being ready to accept them. Your forgetting a part of coming to terms with your sexuality in this dynamic is literally rationalizing if proximity to the guy you like is due to attraction and percieved as gay, or just normal bro activity.
That's the issue, though; they're gonna end up together, so it means him becoming more open to things is just coming to terms with his sexuality, not a straight guy just leaning how to be platonically intimate with another guy.
Aside from bi-erasure, the whole story seems like it's gonna be about MC coming to terms with his sexuality. And while that makes for a neat story, I'd much rather someone going through that is straight and becomes comfortable with his sexuality--this story kinda sells the whole "closeness between guys has to be romantic/sexual" thing.