Also, important is what you play on that guitar. If you find that in certain regions of the neck that the match is not that good, you need to take the references in that region.
Using a tone match for one type of guitar on another can be done provided the required adjustments in eq, drive, and master volume changes are small. That's because a lot of controls are cross coupled and nonlinear over their entire range, but practically linear in a narrow band. When two guitars are grossly different, then the tone match doesn't hold together. I found that if I chose a guitar that is truly between a Fender and a Gibson, like a 513, for the sampling guitar, I can get something that's darn near usable for both. It just depends on whether gross adjustments are required to go between them.
One thing that I haven't tried is switching the tonestack to active. According the manual, the active stack is not cross coupled.