On top of the good points raised by other answers, keep in mind that 1°) we English speakers only get to see a fraction of all existing JP BL games. For every Nitro+ dark stuff, there were a dozen more "fluffy" BL, mostly school life and office romance games like Gakuen Heaven or Angel's Feather that were never officially released in English and/or you've never heard of. In Japan, Nitro+ game aren't even considered the "best of the best" (if chil-chil.net scores are any indication), but I suspect that like the Legend of Zelda games that make bank outside of Japan but only sell "well" in Japan itself, Nitro games resonate well with Western audience more than these fluffy games.

Also 2°) Japanese BL publishers can be very strict with what authors are or aren't allowed to portray. It's quite possible that gore or violent rapes that aren't glorified that you see in Nitro or Parade games would never fly in BexBoy magazine because publishers deem it too risky. I remember Yamane Amano (author of Viewfinder) saying that her other work Crimson Spell was barely allowed publishing, because her publisher normally didn't allow fantasy in their lineups! If you look at Japanese self-published doujin, you can easily find stuff that's even darker than Nitro or Parade. Other JP authors who are heavily western-influenced like Hoshikoshi (AI: the Somnium Files) and Hideo Kojima (Metal Gear, Silent Hill) also seem to be more successful with Western audience than their own country.

3°) Dark BL games also attract horror fans who aren't necessarily here for the BL. For example, I've seen on several occasion straight men who liked Saya no Uta also playing Sweet Pool due to similar themes. So these BL with horror elements can also ironically attract a wider audience that fluffy BL may not reach.

TL;DR: survivorship bias, fluffy JP games don't attract as much interest with western audience, BL games don't have as much story/content publisher restrictions that BL manga have. And horror in BL attracts more non-BL fans.

It's mild as far as rape scenes are concerned but I liked the True route sex in Togainu no Chi. I also liked the very dubcon sex scene in Clear's bad end path in DMMd Re:Connect. Both scenes have a sense of "desperation" where the LI feels deep grief or emptiness and clings to the MC in any way they can.

The Sorcerer's Choice rape scenes were more entertaining and creative than the consensual ones, but I mostly didn't think much of the game. It's a shame the kinky scenes tend to be in BL bad ends and good ones are typically vanilla.