Mysterious Islands are already kind of broken on their own, so whether an effect that could still function with a fort present would break things even more will depend entirely on the effect.
Any part that was meant to function while a fort was sitting on it would have to be clearly stated as such in the text, so it could override the standard rule that normally shuts them down.
For the most part, that rule exists to avoid weird interactions with the various effects that manipulate treasures, and more generally to prevent ships from easily farming effects from a protected position.
I think it could be pretty neat to have some MI effects that would only function while a fort was present. There’s a lot you could do, from simple boosts to cannon rolls/ranges and defensive bonuses, to more complex things like making it more costly to build there, or having ongoing negative effects that have to be dealt with to keep a fort in a prime location.