It's important to understand the nature of the Mac's knob. It's simply a pot at the input. It's totally passive. There are no "electronics" before that pot as you enter the Mac. So whether you turn down the SMS pot and turn up the Mac pot, or vice-versa, it's the same basic idea. Jerry's Fender had not pad-pot, so he came out of the Fender pre full strength and used the Mac pot to attenuate. That's why I say that people with Mac's should crank the SMS rear pot all the way which makes it as if it's not there (like Jerry), and then use the Mac pot to set your master level.
If there is some issue with the Mutron result here, that should simply be a factor of how hard you're driving the actual power or loudness of the rig overall. That dance between the SMS rear pot and the Mac's pot should have zero affect on the Mutron's action. It suggests to me that maybe under one of those conditions, you are driving the Mac louder than with the other.
... and it's just like any other day that's ever been...