Man, you sure took in a puzzler there! Very few times have I been unable to back out the set screw on the 'standard Fender Skirted knobs as used on the 94 Twin Amp. I gather no signs of moisture or rust on the set screws. Rust & time will yield them to be a PITA, but nothing like what you found here.
I agree with your assessment....how the dickens could a front hit on a knob drive the shaft back thru the bushing to take out the pot, since the knob would bottom out against the chassis front panel. All those pots use an 11mm hex nut. 9/16" nut? yes...WTF? I've had to replace that push-pull volume pot more than once, but never encountered what you've found this time. I've certainly had set screws strip out, but locked into place? Only thing I can think of there was someone must have thought using loctite on the set screw was the thing to do.