As far as I understand it, and I am not a lawyer, this is exactly the same finding as the ECJ made against the European Basketball Federation a few years ago when it banned certain players after their participation in an unlicensed break-away tournament. The court found the action of banning the players was illegal because the Federation didn't have any criteria for approving / not approving external (ie those not operated by the Federation itself) tournaments. The ruling wasn't that the Federation wasn't the governing body for the sport in Europe, or that it couldn't run its own tournaments, it was that the Federation couldn't disapprove of an external tournament purely because they didn't like it, or because it devalues their own competition. Any approval criteria, of course, would have to be required for the benefit of the sport, not for the Federation's own benefit.
This is why I say the UEFA / ESL ruling is consistent with the previous ruling. UEFA tried to punish (in this instance) the clubs for joining an external tournament which didn't have the approval of UEFA. So I am not surprised at the ruling.
What the ruling doesn't say is that i: UEFA isn't the governing body for all football in Europe, ii) UEFA can't operate its own tournaments and iii) and can't disapprove an external tournament if it doesn't meet UEFA's criteria for licensing tournaments (again with the caveat that the criteria must be for the good of the game and support the European Sports Model).
So, to answer your questions, imho: i) UEFA can stop an external tournament within the UEFA / FIFA structure if it doesn't meet its criteria for such a tournament, and ii) UEFA can't stop a tournament if it is a break-away from the UEFA / FIFA set- up.
Of course, in case i) the ESL would challenge the criteria and that would take another two years, and in case ii) UEFA / FIFA would, I imagine, ban the clubs concerned (including, I would think, women's and academy activities unless they are spun off) from participating in FIFA / UEFA / domestic league tournaments and ban their players and any officials involved likewise, and then that would be challenged by the ESL in the courts for, say, another two years.
Difficult for me to see how it gets off the ground, really, if UEFA gets its ducks in a row with sound criteria set for the benefit of the game.
All my understanding, which may be absolute bollocks, of course.