When I first received my Axe FX-II, I used my Strat that had mini humbuckers in it and the level was about 51.1%. It would tickle the RED if I was strumming hard (something that I normally do once in a while) and had no problems. When I switched to a guitar with active humbuckers, I would have to turn the volume down on the guitar or else I would be in the RED for the majority of the time to where the cleans sounded dirty.
After reading some random thread on here, I decided to use the guitar with active humbuckers as my baseline. Now I am set at 33.3% however, that brought the output volume of the Strat way down. Changing to single coils probably added to the issue but it also gave me a reason to learn more about the cause & effect that every action has with different guitars that no two are alike (body shape & pickup choice).