No
Train sex /is/ a cliché trope. I'm not saying this to be rude, but have you never come across yaoi with chikans (a person who engages in public molestation, especially in crowded trains)? I'm sick of it, especially when mangakas use it in PWP. It's not sexy, less so when the perpetrator is some 40+ year old creepy salary man (the first person to molest the uke falling under that description).
Secondly, the OP pointed out which elements they considered cliché, so it's a bit rude to twist their words like that. They didn't say "ghost semes" and "train sex" were clichés. They said it was rape leading to love + multiple rape and reciprocation for the rapist that were clichés. And to be honest, they're not wrong. Rape = love is a dangerous, overused trope in yaoi, examples being Viewfinder, Junjou Romantica, Love Stage, and Koisuru Boukun, all rather popular yaoi mangas.
I liked the sexual ghost idea, which intrigued me more than the common succubus/incubus/other type of sex demon featured in mangas. So I'd agree with you that a ghost seme isn't a cliché, even though this isn't the first manga I've read about a ghost partner. But the OP brought up valid points, and I agree with them and the rape clichés also made me dislike this manga.
I'm just so glad I'm not the only one who feels this way… It also made me really made that he didn't save him right away just because he wanted to see him with different expressions. I've read parts of most of the other examples you've listed too, and I don't understand why people like those series so much…
(By the way, what does "OP" mean? And "PWP" for that matter…?)
Didn't like the manga, cliché 1: Seme rapes the uke, and the uke fall in love, cliché 2: Seme rapes the uke many times. And the Uke have feelings for the seme, but think that the seme dont care about him(uke), then the uke gets sick and the seme dont rape him (while he is sick) takes care of the uke, and the uke is like omg he didn't rape me it means that he loves me.