I'll vote 'ears' too. I usually do all my setup with the pickups cranked way down, that way I know the magnets are not going to effect intonation. Once everything is done, then I adjust the pickups for sound and balance.
The Fender guidelines are good starting points for Fender gear, but they're just meant (in my opinion) to get the guitar sort of playable and out the door. Just a starting point... If you try to apply the same rules with something with monster magnets, you'll fight the darned thing and have a devil of a time figuring out what's happening.
Yet another hobby that is completely out of control...