The amount of self-reflection and critical thinking about how your manga favorites all tie-in together is impressive. I will try my best to match your passion with my own! I have read some of what you have listed here, but based on what you wrote, I have a couple that come to mind.

• Love After World Domination - A Romeo/Juliet style forbidden love between the Red Ranger and the rising star of the evil organization he is fighting against. This one is super wholesome and hilarious. There was a recent anime adaptation as well that did a pretty good job. Unfortunately, when the anime didn’t really drive sales of the manga, the series was cancelled :(
• My Wife Has No Emotion - A story about a man that falls in love with his robot and their daily lives. This relationship isn’t often portrayed as overly taboo, but it is a recurring plot point that people find it unusual. Overall though, this series is super cute.
• Domestic Girlfriend - If taboo relationships are what you are after, then this series has it in spades. There is a lot that can be said about this series, but it never gets boring. Just when you think the story is setting into a rhythm, some plot twist will blindside you and leave you expecting to turn the page and realize this was actually all a dream sequence, just to find out its all real, and it’s not stopping.
• Konjiki no Word Master - Stop me if you have heard this one: a group of students are summoned to a fantasy world, and one of them doesn’t seem to have useful abilities so they are released from the responsibility of becoming a hero and free to lead their own life, however, it turns out their ability is actually the strongest. The premise is very cookie-cutter for this one, but I think that this story fits in with others you list (like the speedrunning one, which I am also a fan of) in that the MC is constantly breaking the common sense of those around him. His magic is unlike anything anybody else has seen before and it allows him to forge bonds with groups and in ways that nobody else has before.
• I Shaved. Then I Brought a High School Girl Home (also known as Higehiro) - I am not fully caught up to the manga of this series, but have read the novel version (I think there was an anime adaptation as well). I find this one fascinating. It is a story about a salaryman that is drunk one night when a runaway JK propositions him in exchange for a place to stay. He shelters her, but instead of what she had initially offered, he kind of becomes a pseudo-parental/husband figure to her. He helps her deal with past trauma and get back on her feet while she helps him deal with things in his life. There is a complicated web of relationships woven through this one and they are all messy. Very much in line with taboo things as this adult has a complete stranger runaway high school girl that starts essentially acting as his housewife.
• Kino no Tabi - I linked to the anime here since I have only seen the anime, not read the manga/novels for this one. Also, there is a previous anime adaptation as well. I watched both and they both are great, but I think most modern anime watchers would prefer the newer series visually. This series is an anthology of short stories about an adolescent named Kino traveling across their world with their talking, sentient motorcycle companion Hermes. This one is perhaps a bit different than the others I have listed here, but during Kino’s visits, they often run into moral dilemmas and have to decide whether to intervene in this country’s affairs/customs as an outsider, or to instead remain an observer. At times it feels like Kino has a sort of Prime Directive from Star Trek that they follow, but other times they are forced to get involved. It is a series that doesn’t necessarily cover the taboo in the same way you wrote about, but often the storylines that are portrayed and Kino’s response to them can leave the viewer feeling uneasy or unsure if it was the right thing to do. Overall, just an excellent show (both of them).
• Girlfriend, Girlfriend - This manga finished its run not too long ago. I am guessing you might be familiar with it if you are also reading 100GF, but if not, then it is another series in which the protagonist, Naoya, attempts having multiple girlfriends at the same time. The ensuing humor and antics are really great and Naoya is a great MC (not like Rentaro though, Rentaro is the GOAT). A recurring theme in this series (basically, the recurring theme) is the taboo/unconventional nature of polyamorous relationships and the complications it presents. There is an anime adaptation that just finished up its second season, but I prefer the manga for this series.

Alright, I am sure there are other series rattling around in my brain that would fit here, but after just waking up, this is what I am capable of remembering and writing somewhat coherently about. If I think of more, I will tack on another comment. I am sure others in this community can chime in as well.