I used the Universal Ren'Py Mod, and turned NTR off on certain parts to see the difference, the main thing changed is the dialogue, of course some scenes are also different, but most scenes still happen, just you don't have any chance of any NTR happening is all.
The dialogue differences usually boil down to, if NTR is on, loyal Lara will still have thoughts when she sees other guys she likes, and will thirst for them a bit, so basically with NTR on, she window shops quite a bit, with NTR off she doesn't.