High opinion vassals will still leave factions. I don't know if the thresholds are exactly the same as they used to be but in my experience it does happen. The differences are that it's now more difficult to make vassals happy and favours can be used to bypass this for factions (note that spymaster action could always be used to force others into factions regardless of opinion, and remains).
Also, don't forget that you can just capitulate to the raise council power faction. All it will do is allow council to vote on an extra thing. It has much less impact than the old lower crown authority faction and I regularly capitulated to those if I wasn't trying to get up to Primogeniture or something like that. It's only if you're aiming for Imperial Administration that these factions become really annoying, but even then it'll put you back only ten years (as opposed to a generation for the old crown authority).
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