First off, I have to say that I am super impressed with the Variax Standard. I actually bought the JTV-59 about a year ago and decided to return it based on the slight latency in alternate tunings and the inability to pinch harmonic. As someone who is into metal, pinch harmonics are kind of a big deal.
Since then, I bought an open box version of the Variax Standard in order to give it another try. I am really glad that I did. I am kind of thinking about getting rid of some of my other guitars because I haven't played them in a week since I got this thing.
To start, when I am in standard tuning (using the alt tuning knob) I have 0 latency and pinch harmonics work excellent. I even physically tuned the guitar down to Drop C (CGCFAD) and left the knob on standard tuning, again 0 latency and pinch harmonics work excellent. I tuned the guitar back to standard tuning and turn the alt tuning knob to Drop D, my custom Drop C preset, or even baritone and I get a little latency (still usable) and warbles when I pinch harmonic. It is most noticeable on the 5th and 6th string, but happens on other strings as well.