I'm really confused about the true ending and the plot behind, and not sure this is related to the translation or it was made vague on purpose. Is there any discussion going on about it somewhere?
I'm sure there's discussion here and there, but any discussion in this thread should cover the basic understanding of the plot. From what I know, the entire plot is about a time loop started by Yuki and "Homura", and how it canonically ends and what it all means depends on who you ask. Definitely Cthulu mythos involved. We're hoping to get answers in the all-ages spin-off.
Is this really netorare? I mean, the lover stealing scene at the end of the game, netori to be more precise. And the rape scene where we choose a different companion at the beginning, and then after that the rape scene shows "no romantic relationship has been built with the character being raped yet" is that considered netorare?
Definitely a lot of cheating, for sure. If we're being precise, there's some NTR in-game. (Tapes, NTR route, special rest events) If you want to go for a meta explanation, then yes there's a lot of it. For example, you as the player saw Mia and Yachika hook up the last playthrough, so you decide to make Mia your lover in the next. Or you like Rikana but have Seijiro end up with her instead. Lots of hoops to jump through.