In most Mesa amps, the Master is before the loop, so it is really more of an FX send level control, not an output master.
Again, in most amps, there is signal bleed around the FX loop because each preamp tube is actually two amplifiers. There is almost always a tube that uses one channel (A) before the loop, and the second channel (B) after the loop. There is crosstalk inside the tube, both mechanically and electrically. So you get signal bled around the loop, and it is not attenuated by the master because the master is pre-loop.
This causes problems when you use digital effects in the loop, because you need to have a 100% series loop, and the signal bleed makes even a series loop just a little bit parallel. The problem is most troublesome when running low volume, because the signal bleed is more obvious then. It gets totally swamped at high volume.
Hope that helps.