Honestly I think it's difficult to tell, there's a big difference between games focused on NTR and those where it's just another tag. There's some pretty popular games on here that seem to fit the bill of having it but not revolving around it, e.g. "A Struggle with Sin".
Having said that, I completely agree with you that giving players the option to opt out of content is usually desirable. There may still be cases where some content can't be avoided for genuine story purposes, but those instances are probably rare.
As an aside, I think focusing overly much on what you (meaning a random developer) might think are the most popular tags and trying to crowbar a story around them seems like an overly cynical way to go about things. Unless you're super talented the result probably wouldn't be great. Plus I like that there's a large variety of content on here, including very niche things I have less than zero interest in.
What I think is that the harem shouldn't be the main focus of this game: it's clearly an NTR or sharing game, so in my opinion the harem serves more as an add-on to the game.
From Dev comments, it seems that NTR and sharing will focus on side LIs. I'm not sure if this means that the main LIs are going to be left out. My opinion is that the Dev should make the NTR and sharing extendable to the main LIs (possibly avoidable, to widen the options): People who enjoy these fetishes will find it frustrating that it only focuses on side girls (while many of those who don't like them will avoid the game even if the main LIs aren't touched): Including the NTR and sharing in the main LIs will make the game more attractive to the public to which it's directed, and making it avoidable in the main LIs will broaden the base of people who can enjoy it who don't mind sharing and NTR happening to the side LIs as long as they can keep the main ones "safe". Of course this won't get the most hardcore harem fans interested in the game, but it may appeal to many others who aren't as extreme.
On the other hand, I don't know if this is the only possible ending, but from Dev's comments, it seems that the intention is that, at the end of the game, only the MC and the main LIs (and not sure if any side ones) remain. I can't say from my own experience, but it doesn't seem like the kind of ending that fans of the NTR genre are looking for, but I could be wrong. My opinion is that this game needs an ending that suits the tastes of the NTR and sharing players, and if at the end of the game all possibility of NTR and sharing is eliminated, it's possible that quite a few players feel disappointed.
The fact is that the Dev should think of several endings that can please the different types of players he is appealing to: those who like sharing and NTR should be able to enjoy one or several endings according to their tastes. While those who have decided to protect their LIs from NTR and sharing should be able to be rewarded with an ending according to how they played.
But it's just my opinion.
If you don't like NTR so much not sure why you are going thru the thread of an NTR game. Are you an anti-NTR warrior that runs from NTR game thread to NTR game thread trying to get the dev to get rid of NTR?
Like you said yourself there are more people who want to play the harem games then the NTR games so why come to a game you apparently have zero interest in playing because it has NTR to make a comment about how you don't like NTR?
Read my reply for RedTomato and then if you continue to think that nonsense I will answer you.
EDIT: I'm just trying to express my opinion, which may or may not be useful to the developer of the game (it will be up to him to decide if what I say is good or not fits with his vision of the game). If someone doesn't like it, they can always not read it, but I'm not going to stop giving it to please them.