I play on StingRay since 2005 and I must say that factory specs for pickup height are too high for me. I think that it depends on your string height. Mind is 7/64 on E and 5/64 on G so it's a 1/32 difference between them. So I set my pickups the same but way lower. For me for medium gauge strings it's 8/32 on E from pole piece to bottom of the string and 7/32 from G. Clean and even sound without any strange sounds of "chorus" or lack of sustain on last frets. Musicman humbuckers have very high output and with factory specs I can't setup intonation with tuner because there's too much magnetic field interfere to string. Especially on bass site. I hope it helps and make sense.
I ended up lowering it. All the MM's I have owned were even from side to side. All were bought used, so maybe they had been adjusted before I got them.