If you're not aware of what my Comanche VI+ is/does check my Gallery and Project page for info. Basically my Comanche VI+ is wired to emulate a standard Comanche or Comanche V, Comanche VI, and a bunch of other sounds that the production guitars can't. I ran it with split Z Coil pickups with the standard bar magnets for a while and have some insights about why a V and a VI sound different.
It's not the switching. A Comanche V runs each Z Coil pickup as a full pickup with the 1/2 coils in series, then you have standard 5 way switching. The impedance of a single pickup is about 5k, 2 pickups in parallel give us 2.5k. The guitar is a high impedance guitar.
The Comanche VI runs each 1/2 coil in parallel with any other 1/2 coil. You have to run at least one treble pickup with at least one bass pickup to get the full guitar sound, those two pickups in parallel would give us an impedance of 1.25k. Switching any other pickup on in addition continues to lower the impedance even more. This makes a low impedance guitar which doesn't have an impedance matching transformer.
Low impedance guitars sound different than high impedance guitars. A low impedance guitar sounds like a hi fi instrument.
It's not the switching in the Comanche VI, IMO.
If you own a VI and aren't happy with the sound find yourself an impedance matching transformer, similar to what the Les Paul Recording guitars had. It will suddenly sound more "normal".
I was disappointed with the Z Coil sound for a variety of reasons, the promise of split pickups (EAD through one amp/effects, GBE through a different amp/effects) remained a big enough motivation for me to fix the magnetic design. Summarizing I removed the bar magnet and movable pole piece sections and selected magnets that fit into the remaining space of the stationary part of the Z Coils. My modified Z Coils now sound like Fender single coils, I'm still adjusting to the pickups but my initial impression is its sounds like my Strat and/or Tele guitars. Finally splitable coils with the right sounds. Before I could only get that sound by leaving magnets out of a full size Fender single coil.
My Comanche VI+ has more than 2x the wiring of a Comanche VI and 8 switches vs 6. The sound is anything but hifi.