I haven't had a chance to work on this issue. What I can tell you is that I could not create the tuning using Variax Workbench. I didn't try doing it manually using the guitar only so maybe that's the trick. I just figured if Workbench can't do it, it couldn't be done. The tuning I'm trying to create is E1/E2, B1/B2, E2/E3, B2/B3, E3/E3, G#3/G#3. I don't recall on which model I was trying. Probably the Rick 12-string, bridge pickup.
No, you cannot do this from the Workbench - that's the point. The Workbench predates the Variax JTV electronics and cannot swizzle any of the new features! The older model guitars had alternate tuning intertwined with modeling and indeed could not do what you are trying to accomplish. The JTV has these concepts completely separate. Just as the built-in Open D will shift all 12 strings of the Rick models (or acoustic) to a what a real 12-string would do, you can "train" it to replace one of the built-in alternate tunings with your desired Open E and do the same. You do not even need to be in the 12-string model, as the "training" operation works at a very low level. Warning: It is a bit fussy and I find it can take several tries before it correctly tracks your input!
The procedure is documented in the JTV Pilot's Guide and there's also a short video on the Line 6 website.