I never use factory setting on any guitar. I don't even look at them. I start flush with the pickup rings/pickguard and adjust one at a time up/down 1/4, 1/2, and full turns at a time until it sounds best to my ears. Then tweak to taste for balance levels between both pickups. A couple days later I'll go back at it with fresh ears to make minor adjustments.
Typically the neck is somewhere near flush with the pickup ring, that's where the 5815LT neck shines to me. The bridge typically is a little higher, depending on how how hot it is. The 5815LT I run even higher, but honestly I've swapped it from the bridge with a 5909 and a 5708 in two guitars with LT. The third is about to get swapped all together, probably humbucker P90.
There is no right or wrong answer when it comes to pickup height. Whatever sounds best to you through your rig and playing style.