That's correct. The physical position of the knobs is ignored when a patch is recalled, except the master volume, which isn't programmable. When you move a knob, then the pre-programmed setting is over-ridden and the sound reflects the physical position of that knob, but the other knobs are still ignored (until they're moved).
I also have a refurb 60VTX from MF, and I'm favorably impressed. :)