To put it simply, no. The first playthrough allows only one relationship at a time, and NTR only happens when you start the vanilla relationship and allow her to get taken by the BBEG. So to unlock all the vanilla and ntr endings, you need to play through multiple times, or edit the save files yourself (so, maybe yes, but not by playing it).
The main way to heal is by sleeping in hotels. There are recovery points, but they're not in every area, and they're always just before a boss fight; AFAIK there isn't one in the Orangette factory.
I thought the game was bugged because I couldn't use the bed in the hotel. Wow, never seen an h game force you to rely on recovery items.
It does not lock you into the ntr route. You can get both the lewd crests and the nipple piercings and still get the love endings. (The choice that locks you into ntr route is after you get a love confession scene before final town.)
You need to progress a bit before you have the option to talk to her like you can with Serena IIRC.
