Getting back to NTR there's a scene with Yukihime where she sleeps with Hakkin Dasan to recruit him to fight against Rance temporarily. I believe that Sakamoto Ryouma can become either a guy or a girl. If she becomes a guy she sleeps with Kawanoe Mine I believe and if a girl she sleeps with Rance. It's possible that Omachi may sleep with Dokuganryuu Masamune, but I don't recall. There's also a relationship between Nanjou Ran and Houjou Souun. I don't recall them actually sleeping together though.
I feel that there is Japanese history in this game mixed in with Yokai. The different clans seem to be close to ones that really existed in the past, but have been changed. It also likely draws from Japanese mythology with Yokai and other mythological creatures.
Leila has one if she goes below 25% in a fight with the monster army
Kenshin has one if you don't save her in time (It's Lesbo though so does it really count)
Isoroko ALMOST has one in her route (depends on how you view NTR)
Yukihime has 3 technically (One with the hermit and 2 more when she's fucking people for political gain)
Kouhime (though not a heroine in this game, has one as well)
The rest are just implied NTR, there aren't any visuals for it. Like when a certain quartet of brothers steal your commanders