Not sure if I sent this link yet already cause mangago is kind of wack but
https://www.mangago.zone/read-manga/sheep_s_mask/
I read that one and I really dislike it because its essentially rape porn interspersed with a backstory. It feels gross to read without having any real appeal except revenge. And for killing stalking, I feel like the rape is sort of just another way of showing the guys being tortured by a psychopath
It's not that the rape itself is well depicted in terms of the emotional and psychological effects it has on the uke, but it does explore the toll it has on the seme later in the series. It was a refreshing point to see rape being addressed "properly" even if much later. In this case the seme is struck with huge feelings of guilt and self loathing for what he did to the uke, and spirals out mentally due to it. It's in hidoku shinaide (rape in volume 1, chapter 1 and the reflection in volume 6). The character development game there is great and one of the reasons why it's one of my favorite mangas and couples of all time.
I read it because of what you said and yeah the character development is well done, but he feels bad for the last few pages of one chapter and then half of another. He literally showed no remorse until a side character almost got raped as a plot device. Him refusing to have sex one time and acting moody isn't really the act of a penitent. And right afterwards they had sex and moved right on to the dad storyline. That's pretty much the author going "well we're going to have to address this at some point" and then moving on as soon as possible. I honestly feel like the story didn't need rape in it, if they wanted a redemption arc they could've just had the top be an asshole not a rapist bastard. He also just shifts from rapist bastard to a persistent sex fiend to emotionally abusive and cold to a doting possessive top. He goes from incredibly unlikable to a stand up guy within like 3 chapters. Honestly the handling of the rape really drags this from like an 8 to a 5 for me.
I just think that for a semi old school manga to even address it at all is great. Its actually not the only scene where they address it it's just the main one. An although I do agree the the seme was more than an asswipe at the first volume the more you read in the more grounded he gets. But at the end of the day this is just my two cents. If you agree with me of not is beyond my control ╮( ̄▽ ̄)╭
Name more than two bl/yaoi where rape is depicted well. I can name one, I can barely name two, but I can't name a third.
Zankoku Na Kami Ga Shihai Sure (the best depiction of rape I've seen in media in general)
Boy meets Maria
(Honorable mention goes to J no Subete, it's listed as yaoi but the character identifies as a woman, so not really)