The master output is after the FX loop and the FX loop is tube buffered.
Typically, running through the FX loop bleeds off a little bit of top end detail and in the process smooths things out slightly.
Additionally, if you crank the channel masters too high you'll start to overdrive the FX loop.
I typically run channel 3 as hot as I can get it without overdriving my delay pedal, then adjust the other two so that they're balanced. Usually this has channel 3's master volume around 10:00 in Mark IV mode and slightly higher in IIC+ mode.