Wasn't NTR; he wasn't even remotely interested her in that way. Which honestly brings me up to the reason I never actually finished the original game; MC was pretty garbage and hard to like. His Arachnophobia made him scared of spider-girl constantly, and that "NTR ending" you mentioning is her hooking up with his best friend and classmate instead, because they were childhood friends (pretty sure he even encouraged said friend to do so).
The annoying part was that some of the writing in general was meant to be thought-provoking but it lacked any original message beyond "don't judge based on appearances", and to emphasize on that point, they make the MC be some scaredy-asshole who complains incessantly about getting a free hook-up to a wife of choice because they're powerful monster girls, and is freaked out by how they all look (the robot girl is the only one he deemed normal looking). He was basically made out to be a character who does an eventual 180 to liking them, but it's way too sudden and he still acts cheeky and childish for his age. To be honest, he's completely detestable. The rest of the game is just full of ridiculous shit, like having sex with a giant mecha girl, or sex with the equivalent of a vending machine (note that this last bit isn't a complaint, just pointing it out).