For your future peace of mind, if the tag "futa/trans protagonist" is there, without "male protagonist" or "female protagonist", futa is going to be non-optional.
Very ambitious and risky going for both harem and NTR in one game. I wish you the best of luck with it, and I'll definitely be trying this one out shortly.
A couple things to keep in mind, though. Splitting the content between opposing fetishes will lead to a lot of people complaining that their preferred route doesn't have enough content, since everyone would prefer you put 100% of your time into their preferred fetish.
The Venn diagram of people who will play the dom(harem) and sub(NTR) routes have virtually zero crossover, so you're basically making two separate games, for two separate player bases. It's vitally important that you don't allow either route to bleed into the other. The harem fans are especially touchy about this. If there's even the slightest hint that one of the LIs would consider looking at another character besides MC on the dom(harem) route, most of the harem fans will storm out.
What you're attempting isn't impossible, but you should be aware of the difficult path you're putting yourself on. You're going to get a LOT of complaining from both sides, but try to grin and bear it. On a final note, being upfront with info regarding the more controversial fetishes, such as NTR, swinging, sharing, mind-control, corruption, etc., is extremely important. If it means giving spoilers, it's most likely worth it to avoid heavy backlash about fetish content. Surprising your players with extreme fetish content will hurt your game much more than spoilers will. Likewise, if those fetishes are less extreme, knowing that ahead of time will scare off less, or attract more, players.
