As far as neck pickups being lower, I do find neck pickups sound "best" (personal opinion, of course) low because the higher you have them, the boomier and more exaggerated "neck-y" they get.
That being said, for me, it's about finding a balance. If I'm using high-ish or mid-high output bridge pickups (like the JB or the Custom) and vintage output neck pickups (like the Jazz or the '59), I almost always end up having them at roughly the same distance from the strings for them to balance output-wise at first, and then lower the neck a couple nudges in the mounting screw for it not to sound like boom boom mud.
But yeah, for me, I adjust neck pickups for them to work better with the bridge. Never the other way around. But my reasoning for that is I'm 95% of the time in the bridge, so squeezing the most from that position is my priority.