In the Main Game, Hunter has been described by the developer as a Wile E. Coyote type character, always chasing the girls and instead ending up failing (and increasingly getting injured in comedic ways). The NTR is restricted to the Bad Ends which are by nature designed to be pretty easily avoidable but can also be fully deactivated never to be seen again. There is NO on-going story route that allows for NTR, only Bad Ends.
The What Ifs are voted on, and the NTR fans keep winning the votes. There is, I believe, ONE What If to date that is not NTR, where Sterling embraces his role as harem master and goes hog wild with all the women in sight.
The idea that development time is being taken away from the main game to produce the What If episodes has been repeatedly refuted by the dev along with an explanation of why that's not true, but some people (mostly people who really REALLY hate NTR) refuse to believe him. This has been made worse by the fact the the last few updates to the main game have gradually taken longer to complete. However, that fact was predicted and we were warned about it. The official stance of the dev is that the updates are taking longer because they are bigger, include more girls each time, and have more animations. The official explanation from the dev on why the What If episodes do not cause a delay is that he always had a set work schedule for development of the main game, which he has stuck to, and the work he is putting into the What Ifs he is doing during what had previously been his days off.
EDIT: To be clear, there is metric ton of non-NTR content in this game, most of it beautifully animated. It's one of the hottest games I've ever played. It is also written to be comedic a lot of the time. I personally do NOT like feeling helpless to avoid rivals and NTR, but I never feel that way while playing this. Hunter never feels like a real threat to me in the same way as the NTR threat characters in a lot of other games. He is essentially a parody of NTR characters. He is a hideous buffoon that the women have no interest in romantically and are not attracted to at all. He is a creep that is always lurking, but as long as you follow the story and don't watch the optional and easily avoided NTR Bad Ends, he consistently comes off as comedic foil with ridiculous schemes that constantly backfire in humorous ways.
That is one way to look at it. I just want to say that I like Power Vacuum overall, and was an early supporter because of the comedy, quality, and heartfelt moments with the cast and MC. I even thought the initial method of including optional "parody" NTR funny and innovative compared to the other versions out there, but just initially. It has become something else now. It started as a little "light hearted", relatively, way of including the fetish, while not really denigrating (my main concern) the characters, because it starts with short instance brought about through drugs or trickery of the girls and a MC who choose that path, and like you say restricted to "bad ends". But it "evolved" unfortunately... obviously because of how much money it is bringing in.
While "non-canon", the characters themselves stay in character during the bad ends and the what-if's, meaning that pretty much every female character in the game not only has the potential to become a relatively mindless cock-sleeve, but does so far more easily for the NTR scenarios (albeit, not as easily as your typical NTR), even when initially there is an excuse/lever to push them into it it is still very damaging to their characters as far as the main game is considered imho, especially in their treatment of Sterling in many of the scenarios. One canon part of the game itself that is proof that this is more of a multi-verse reality than random bad ends, is the fact the Gramps did to the MC's dad and his immediate family exactly what happens to the MC in the NTR situations. The MC never has (as is usual with NTR), an easier road (which is realistic, but hardly fair compared to the NTR).
Then add in all the girls first times going all the way, are almost always NTR, and you cannot tell me as a developer that a considerable portion of time and resources (rendering alone!) that could be spent on the main game are not instead being spent on the "What-if's" to bring in more cash overall across a longer development time, at a determent to the main game for vanilla players. I am quite positive the overall content NTR-vs non, is probably pretty even all together, but for a game where that started as non-canon side stuff... that doesn't seem to be the case now. There is also the potentially darker aspect I worry about, that everything happening in the main line of the game, is just a method for Gramps to train Sterling into being a new kind of seducer, one that uses feelings rather than drugs to achieve the same ends. Which while better, is still in it's own way a subversion of the "battle" between the two. Just a theory, but a scary one.
It is what it is and you do what you do as a developer to make a game profitable within your desired wheelhouse, and this is an interesting game. But you are putting a bit more sugar on it all than is fair I think.