Your point on the organisation that the Culture setup "Special Circumstances" to solve the "Paradox of Tolerance" problem and Starfleet having similar issues is an interesting one.

Though I'd say that Starfleet is in itself too "noble" to solve the problems that Special Circumstances solves in the Culture universe (though Section 31 isn't and they do feature heavily in DS9).

Frankly I think that Banks was smart enough to realise that if he want to have compelling narratives in a universe where you have near godlike AI's and everyone (including them) is nice, you need that edge somewhere.

Asher's universe which has a similar premise to the Culture (having come after it) solves it differently, some of the AI's aren't nice or even nice adjacent which also works.