I realize this is a very old thread, but since nobody seems to have actually answered the original poster’s question, I’ll add my 2 cents.
I own a Variax 600, and am waiting for a recently ordered JTV-69s. I’ve been reviewing the the Pilot’s Handbook / Pilot’s Guide as well as the Workbench HD Pilot’s Guide to understand the differences. They are more significant than I realized. There are some Guitar Body and pickup deletions and additions, as well as some streamlining of the 5 position switch.
In the T-Model position - The the Thinline tele is gone (it’s also gone from Workbench HD). The selector switch now makes sense - positions 1-3-5 are now; bridge, both, neck, and positions 2-4 are Widerange Humbuckers (which I don’t think existed in the old Workbench).
In the Lester position - The 58 LP Standard on 1-3-5 is now a 59 and the Goldtop and Custom on 2-4 have been replaced with P90s for the 59 Standard.
In the Special position - The Jr. is gone and the selector switch now makes sense - 1-3-5 are bridge, both, and neck on the 55 LP Special, and 2-4 are the 76 Firebird.
In the R-Billy position - The 56 Silver Jet has been replaced with a 59 Duo Jet. I think the only difference is color so …?
In the Chime position - The 68 Rickenbacker 360 and 66 360-12 have been replace with 66 370 and 370-12. The selector switch still kind of makes sense with 1-3-5 as bridge, both, neck for the 370 and 2-4 for the 12 string. Without going into Workbench the new middle pickup is not selectable, so … weird choice to change models.
In the Semi position - The 67 Casino has been replaced with a 64 (different P90s, I think).
In the Jazzbox position - the 57 ES-175 (with Humbuckers) has been replaced with a 54 with P90s.
These are the things that stood out to me. Maybe some have changed with updates.