Oh, don't worry. The fetish toggle option (when there is content for it) will be very specific about the fetishes. We left a lot of vanilla content such as certain positions as non-toggleable since it doesn't really cause problems but anything that I think can cause negative experiences with players (or if any players ask for a specific toggle), I will add it for.
So for your example. Threesome, MMF, FFM, M(Futa)F, will all be separate toggles. You can either enable them all, disable them all, or have a very specific preference. If 'threesome' is disabled then all the following ones will be blocked because it's a given. If you have FFM enabled but you don't like for example pegging and that scene involves it, it'll also be blocked.
As I said, although it will block/opt you out of scenes, it's the only plausible way of making each individual's experience the best and most diverse sexually it can be.
For Futa characters, we give the player the option to either give them a penis or a vagina. If the scene involves phallus-play and the player picked vagina, the character will wear a strap-on and the scene will play if it detects all the player's fetish preferences are on.
We'll do our best to not only incorperate the fetish preferences in the scenes but also in the story and dialogue too. But I'm confident we won't run into that problem as I don't see any plans of making 'sharing with another guy' a very prominent part of any storyline. If a scene ever happens, it'll probably be a one-off, casual thing that doesn't play a big part and when the player opts out of that, the dialogue will reflect it too.
I do want to stray on the safe side of debateable content whilst also providing things that are more niche. Hopefully we can find an agreeable balance. So yes, I agree with you in that the fetish does apply to not just the sex scenes but also the story and dialogue content.