That is an interesting question, when I think it through the other way, I realize that the main trigger for the NTR scene is actually very subtle; the conversation about Blackmail is mostly the same except in the LC version they just sort of gloss over the actual reason (ie: it doesn't matter anymore) whereas on the NTR version Lydia seizes on what the MC says and they have the argument. Otherwise its pretty much identical all the way, with the only other difference being the scene that happens when you open the door. She's either yelling at the screen or getting destroyed by Pete, all other story beats can be identical.
We're still left with the question of is the NTR canon? If so, why would she freak out on the MC about blackmail. Sure she could be acting, but how does the argument help her cause? Seems like she'd want to keep the MC on the hook. So it makes me once again lean towards her not being the mastermind and the argument driving her off the rails (and in the LC version her love driving her to dive in and help)
So I almost have myself convinced that the paths DON'T branch and the NTR choice is just some very emotional flavor (with effects on the MC/Lydia relationship outcome of course) So basically, you can choose "your" Lydia and keep it within the story.
I guess it works if she is the mastermind too, if you can ignore the weirdness of the blackmail blowup. But in that case she's already pretty heinous so I dunno that it matters too much.
In the end I guess there's three Lydia:
True Blue Lydia (LC + not involved)
Toxic Lydia (NTR + not involved)
Evil Lydia (Mastermind with or without NTR seasoning
So many questions. I hope the answer is half as interesting.