I think what you're describing is how they thought they'd be able to fight through spacing issues - on most coasters that run 3/4 trains you can fire all the trains through and catch them at the end. But three blocks for 8-10 trains with the complexity of the Devil's Snare right before those blocks is a lot for the computer to process.
You may be able to hold a train at the curve, but from what I can tell they can't address spacing for the entire length of load/unload because it's all one system tied to the speed of the walkway. Load/unload is where you should be able to clear all that up - if you had extra blocks at the beginning in the area between launch 1 and 2 in addition to the three at the end, I would think it would be a lot easier to keep the ride in sequence.
I'm no expert on ride programming, it just seems like continuous load was a mistake. I think we can all agree that this thing is beyond complex - I can't think of a more challenging coaster profile than the stretch that goes Fluffy, switch, LIM, spike, reverse LIM, switch, switch, drop, switch.