I play the game almost since release, have 1500 hours in the game, I know it used to happen often, never bothered me... but I 'm quite sure that with all the rework of multiple systems, like the rebel systems and the fort system, this just doesn't happen anymore for other reasons... I also don't see crete/naxos/etc.. breaking free anymore from Ottomans, and that should still happen with the same frequency... (just not under the byzantium tag..).. In general you don't see Ottomans sufering from much rebels because of all their awesome ideas/modifiers (and the fact that they normaly go Humanist first).. So it only really happens if the Ottomans are getting totaly rofflestompt, and in that case a rebelion of byzantine nationalist would not at all be weird... In the past sure, even with 1% chance of rebelion every now and again (because of some bad event or highish war exaustion) on one of the island eventualy it would rebel, but now a days that just doesn't happen anymore, except if the rebel chance is there for a very long time, which basicly means that the Ottomans are getting destroyed...
EDIT: also, what you are basicly saying is that the (historicaly acurate) cores got removed to basicly fix a bad rebel system... But now that the rebel system has been reworked and this shouldn't be an issue anymore anyway (except again, when Ottomans are very weak, but then a rebelion is not unrealistic), why not revert this?