But now rebels pose more threat to neighboring countries rather the the one that spawned them. An example: A major have a standart uprising after a conquest, it cannot cripple him just because he can blast any number of rebels easily, so major can wait a bit and wait until rebel stack moves to neighboring province. When some 20-40k stack moves to a country that can muster 15k at best that means that country screwed over and could only hope that rebels will move away to some other land.
Conquer useless land, let several stack to revolt, wait till they move to your neighbors to screw them over. Let's face it - rebels are not a serious threat to the player - it is a threat to AI. Most players can live through 120%+ overextension rebel spree period easily.
This is doubly bad because it trivializes a designed system early and turns into a micro hassle late. Very often in late game I have to kill enemy rebels that cross border into my land. It's trivial and is barely a nuisance from a cost perspective, but the bad EU 4 UI crops up here again.
You only get "crossed border" warning, you get no actual warning that rebels are near enforcing demands and they don't turn up in your unrest screen. Which is a bug that's gone uncorrected for years. You can lose land to a random small unoccupied province from rebels you killed 3 years ago but didn't notice the stripes without any warning whatsoever.
One might suggest to use the auto rebel hunt feature, but this still tends to tie up units unsieging land before killing the actual rebels, which is comically inefficient and lets easily sufficient troop counts get overwhelmed. More micro.
I'm pretty sure the rebels inherit morale modifiers from your nation, but not the discipline ones. If turkish rebels spawn in byzantium, and Ottomans have tech 15 while Byzantium has 14, the rebels will have better tech and huge morale boost. But, they will NOT get the discipline bonus from Ottomans offensive group.
Rebels inherit tech/discipline, not morale or combat ability modifiers.
In case of separatists they use ideas/tech of that nation if it exists, and yours if it doesn't. Rebels have their own morale modifiers depending on type regardless, probably an artifact to prevent them using your morale while the slider is down etc.