I do the same thing and found out zenith is playing a major role on cartridge alignment. To use vta track for zenith is confirmed but I do wonder too the results of new zenith alignment.I predict another Fozgometer goes up for sale shortly.
Looks like one new function which will be great to have in Version 2 is a Zenith function. I already use the VTA track to fine tune Zenith, so it'll be interesting to see how the new Zenith function reports my alignment. Also, just to clarify, while the software upgrade will be free, users will indeed still need to pay for the new LPs to go along with it.