Is there a runtime JS variable I can use in VWO or Optimizely that Digioh reads to disable pop ups?

Yes, this is possible.

1) Set the following variable in VWO or Optimizely. Make sure this is set on the window object:

window.disable_digioh = true;
window.disable_digioh = false;

2) In Custom JS (Parent) - Before Pop Up Display. Check the above variable, and "return false;" if Digioh is disabled. This will prevent any campaigns from displaying. On the other hand, if Digioh is enabled, then do not return anything from this Custom JS section. So in campaign JS it would look like:

if (window.disable_digioh) {
   return false;
}