I've been trying to figure this out for a while...
The longstanding rumor is that the Allan Holdsworth models use an Alnico II magnet, but if you order one from the Custom Shop, they always come with an A5.
Here's the Custom Shop description:
Having observed the differences in response that the 12 screw pole pieces make first-hand in softening the attack of a pickup, I have to wonder if THAT, combined with the slightly overwound JB coils, which enhances the mids and pulls back the top end just a wee bit, is what leads people to assume the originals used an Alnico II, since it's a bit warmer and thicker feeling/sounding...