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So how big of a difference do you think it would make if the electronics from a James Tyler 89 fixed bridge guitar were in a Les Paul style(either double or single cutaway)? You would probably notice that, but how much would Nate Nobody notice? Would it be easy enough to adjust with EQ?
1- Depends on their hearing and how trained they are at hearing. Big difference for some, barely noticeable for others. Me,... I'd catch it right off.
2- EQ is useful, but would take you only so far.
Many factors, and they all play a role. Because it's an instrument, it there wuill be an affect on the sound from instrument to instrument, for a board programmed for something else. If it were a "virtual instrument" in a box or computer, like they do at CCRMA at Stanford, then that would be different,... no acoustics to deal with.
In a Variax, the program has to acoustically match the guitar it is in, as that is part of the modeling process. So there is no one-size-fits-all in this. Part of the reason we don't do retro-fit kits for generic guitars,... wouldn't work well.