I’m kinda confused on the whole part where he was beating him up bad. If it was what nei...

I think Masumi wants to be liked and loved by Tobita but he struggles to transition their relationship from a purely physical to a romantic one.

Masumi regularly puts on a false smile which indicates that he has difficulty expressing his true feelings. He's been playing pretend for so long it has become second nature to him. (Also people generally smile because they want to appear friendly and be liked.)

However, he is urged to drop the act when Tobita points out the insincerity behind his smile. It's supposed to be a kind gesture toward Masumi - that he can be himself. And in essence it is. But Masumi is rattled by Tobita's accurate observation, having been seen through. He feels exposed and knows that his insincere kindness won't be accepted by Tobita. If he wants them to grow closer he'll have to emotionally evolve.

He knows Tobita enjoyes pain but he doesn't know how to show him affection outside of bdsm play sessions. Thus, he showers Tobita with more of what he likes - rougher and extremer sex. Over time this fuels Masumi's unhappyness/insecurity more and more because he is not truly expressing himself/his desires. He is neglecting himself emotionally and instead once again hiding his true feelings in the hopes of binding Tobita to him by brining him pleasure. (In the manga you can see Masumi go back to his fake smile around the time he chains Tobita in the apaetment. They are most likely practicing bdsm as a lifestyle at that point and will stop once Uni resumes, it reads as consensual. I also think it's sweet how Masumi constantly checks in on Tobita and even brings him the second volume of a book series he likes without being asked.)

That being said, as someone who isn't a sub, Masumi doesn't understand the line in Tobita's head where physical pain becomes sexual pleasure, to him pain is pain. Subsequently he pushes Tobita too far. When Masumi reopens Tobita's wound and Tobita uses the safe word Masumi feels rejected. In his mind now even the guaranteed way to show Tobita affection and make him like him has proven inadequate. He doesn't know what else to do. Masumi's frustration/helplessness reaches it's limit and he throws Tobita to the ground.

Soon after, Masumi requests they have vanilla sex. He has exhausted himself emotionally and seeks reassurance and affection from Tobita.

In essence he is thinking:
"Will you keep me by your side even if I don't present as a Dom every time? Am I just a tool that lets you derive pleasure and nothing more? To you, does my value start and end with being a Dom? I want to have value to you as a person, as a lover, too. If we strip the sex off all the extras, if only you and I remain, will I be enough?"

Unfortunately, the vanilla sex does not reassure Masumi, as Tobita is not enthusiastic during the act. At this point Tobita likely does not understand Masumi's internal struggle because he already loves him. Without realizing it, Masumi had already acchieved his goal months ago - he was standing in his own way. He ends the relationship under the assumption that he won't be able to capture Tobita's heart.

Finally, after some months Tobita seeks Masumi out, confesses his feelings, states that he loves him as a whole and not just as a Dom and thereby successfully bridges the gap their unspoken feelings.

Man I had fun writhing this! These are my own thoughts of course (as a Dom haha). I'd love to hear if others agree or disagree, leave a comment handsome stranger! ヾ(☆▽☆)