So in FCP, I get there is no loss going from MXF => QT. But now let's say I export a QT from that original QT, same resolution, same everything, no filters etc.
What is the theoretical loss or image degradation to that file now?
This might be a little bit off the wall, but here's a trick I picked up in a different forum for spotting compression marks, though you'll need After Effects.
Import the original QT file and the newly made file into an After Effects project. Lay them both down on the timeline and sync up at least one of the shots, so that what is playing on one layer is the same shot on the other layer. Obviously your second file will have cuts, dissolves, etc., but you only need to sync up one shot - not the whole thing.
Once you have the sync for one of the shots, set the topmost layer's transfer mode to 'Difference'. You should see all black. Any grey or white sections on the composite should indicate places in the frame in which the two files do not match.
Going by that logic, if you see any amount of non-black, then the compression has caused a proportional amount of degradation to your image.
I didn't develop - or test - that technique, but I remember reading about it in an After Effects forum. I hope that helped!