Don't worry about it, some readers sometimes just never delve in depth to the emotional struggles of the characters of what they're reading. They never understand what is meant to say "putting yourselves to others shoe", because they lack empathy or just too narcissistic to think that everyone must act how they should.
His parents wanted him dead when they found out he was a Esper. That's what set off his powers if I recall that chapter correctly (too lazy to go back and check). Him not regretting his parents death and his powers activating so early were just two things he faced. A lot of his childhood was spent with him hiding his guide/love interest and that other guy he protected.
I completly agree with you that he isn't a red flag or even close to it. He's a green flag with red polka dots. The worse things he's done(so far) is guilt trip the protagonist a little bit. Outside of that he's very(almost overly) protective of him and steps back if he gets anywhere close to him. Even this chapter talks about how the ML stepped back cause protagonist wasn't ready to know and accept all of him. There is a lot of choice that the protagonist can make here and I have yet to see him forced to make any choices that demean or hurt him or him being TSTL.
I don't find it problematic. He's not violent with him. He doesn't hurt him. There's no rape, no psychological violence. He's a character who faces up to his past difficulties to protect the one he loves. Above all, he fears that he will be seen as a murderer. He hasn't been able to control his powers of memory (and if he doesn't regret his parents' death, it seems he has his reasons. His parents were jerks !). Howoo isn't stupid either. He's intelligent and composed. I don't think you should confuse a malevolent character who makes choices that hurt others (a real red flag) with complicated situations where the characters have to deal with it. Btw, i love this story !
That's just my opinion (for now xD) (●'◡'●)ノ