Hi I have a similar question, so just to be clear:
1) The best way to do your compositing/tracking/replacing of edited clips is to get the cut of the scene you need to compoz in separate clips, exported out of Final Cut or Premiere, probably with timecode? Track each shot separately, compoz, and render in ProRes or format of choice, then send back to the editor and replace, replace, replace?
2) My current workflow takes a cut sequence out of Final Cut, then the Red footage gets rendered out of Premiere to After Effects as one sequence, I do my compositing over an entire scene making new layers and trackers for each shot, then export as ProRes HQ for Final Cut. I find this to be doable when Mocha comes into the mix, but requires extra steps and it is easy to make a mistake. What is easier, then? Keeping track of different elements being compoz’d across multiple compositions, or moving my masks from shot to shot, changing my key/spill settings, and checking my tracks?