We originally tried applying by hand right after the flash. For small runs it wasn't too bad if we used X-Glu. But we eventually experimented with the foil resist and it works pretty damn well for us. Now we just lay down 2 hits of X-Glu with whatever white plates were are using at the moment (150/48 or 180/48) for the X-Glu, foil resist in all the other colors and then it goes down to the sublimation/heat press department (which is staffed by 1 person who can do 288-576pcs a day depending on print size and variety (sublimation, patches, foil, studs, etc...more variety is better for production). There is typically zero problems so long as the correct amount of foil resist is used.
...it did take us a bit of experimentation with the foil resist to get the right ratio. Unfortunately I can't tell you what that is as I don't know. If the shop supervisor pops in here I'll be sure to ask though.
The biggest pain is keeping foil resist ink buckets around and making sure people know to not card non-foil resist into it. Doing it on press was slow and if you weren't insanely consistent, time wise, the pallets would get cool the flasher had to get messed with and the process kinda fell apart. Plus, on an auto, it was awkward to have someone sitting next to head 3. I hated being that guy.