First, there's no 'right' answer: It's subjective as the tone will change somewhat the closer or further away the pickup faces are from the strings, and whatever tone you like is what's right for you. There is no 'factory' height from Santa Rosa.
Having said that, aren't the strings hitting the pickups when you play that 'funk' style of yours?
No wonder you had to put padding under them, you must have been at the very end of the height screws' length!
This would add some noise from the contact of the strings on the pickup shells, and in general, even Series pickups will sound a bit 'hotter' the closer they get to the strings.
Generally, that's very close to the strings. On my PJ Elan the bridge J pickup is around a 1/4 clearance, the P pickup about twice that. On the BigRedBass with FatBoys, they are around the fat side of 1/2 clearance. With the exception of the P pickup, I run them equidistant under the B and the G strings. These are, incidentally, unfretted measurements.
The action is .20 nut height at the G, .25 nut height at the B, .012 relief, and 1/8 string height over the last fret, running a .45 to .128 string set. Basically straight, a little relief let back in to cure the buzz, and a slightly high nut (an Anthony Jackson suggestion).
It's important to think of your setup in numerical values, once you find what's right for you. Then you can always adjust to those numbers when you change to different strings, the weather changes, it's been in the case for months, etc.
From a noise standpoint, I would not run mine that high, and I wouldn't want to scratch up the pickup shells, but that's me. You certainly will not lose any gain running them lower with the trim pots to compensate, but again, it's all up to you.
I like mine to play easily, stay in tune, and be quiet. If they can't do all three, out they go. Don't have that problem with Alembics, though . . . .
J o e y