Eddie was the ears, the player, who knew exactly the sound he wanted, and also knew how to communicate it to the designers of the pickups and the guitar to result in the end product. Maybe "producer" or "advisor" would be best? Not really sure, but it's no different than the input that people like Steve Morse, Steve Lukather, and others have had in the design of their artist models with EBMM, though I would say the stakes were radically higher. Eddie was an experimenter, much in the same way that Les Paul experimented with all kinds of things.
The pickup set for the EVH / Axis is honestly one of the best pickup sets ever designed for a 25.5 scale tremolo guitar. There is a reason that it keeps showing up on other guitars, and that the pickups that didn't get chosen are also extremely popular. It's also amazing how part of it was "unintended consequences", as the entire reason for needing the "air" technology on the neck pickup was because Eddie's use of a drill to play was what would kill the magnets in the neck pickup, so they needed to use more powerful magnets that wouldn't get degaussed, but figure out a way to have the sound and feel of a vintage A2 magnet.