The 2d12 spend isn't the only reason to have those large dice in the pool. Spending them gives the players XP, so that's a big thank you right there. But I agree, if your Watcher is being a jerk at the table, mechanics like this are going to seem like agency-stripping mechanics.
So, my advice: make sure you come to an agreement at the table that you're all trying to have a great time, remember that the dice are all out there for everyone to see and that the Watcher is himself restrained by certain mechanics (rather than given free rein GM fiat), and if you think things are drifting toward no fun, make a point of saying so.
For myself, the 2d12 scene-ending rule is there for when a fight's dragging on, and I want to end it and move to something more interesting for the table, or drop a dramatic comic-book style scene cutaway (and probably have the bad guy escape). I have better things to do than hose players.
If you can manage without it, that's terrific.