When you deactivate M/F/F you're not gonna see the action and usually it also means it never happens. Since Fuyu and Tomoe are maincharacters and it is part of the HAREM story, the whole threesome thingy is only skipable. So even with turned off kinks the threesome happened but as I said, you're not gonna see the action.
In first case, this is a harem game and the final goal should be to get all the girls into your active harem.
There of youre will be different routes at the ending where you maybe just decline the whole harem thingy and only take one or two girls. This is up to you. When we release the Characterroutes with sandboxish elements you're also able do get more time for free roam and focus on the girls you personally prefer.
But for now you need to follow the story. Sowwy.
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Also: A statement about Yuki: