With the strings fretted at the very last fret, my P pickups start out being set at 3/32" from the strings. The pickups end up being set higher on the inside and lower on the outside, to match the neck radius. Then, minor height adjustments are made to even out the response a bit more. I ususally end up setting the G string side of the D/G coil a bit closer and the E side of the E/A coil a bit farther away.
Putting the pickups too close to the strings can affect the intonation of the bass. Strong magnetic pull on the strings can make the bass play out of tune.