It's a difficult one really.
It all depends on the pickup, some have a more neutral response and are geared towards reacting with the wood, where most pickups are sold on offering you a certain type of sound.
The bigger companies tend to go with the lattter to cater for all, whereas smaller more bespoke makers will opt for the former.
It's worth a little online research, you just need to know what you're looking for.
Don't dismiss the smaller guys, they can offer some amazing sounding pups, back in their early day's for instance, Kent Armstrong made some great pups, but as they've grown bigger they're starting to lean towards the global market.
Search out someone who you can trade ideas with and can make you your ultimate custom pickup, they're hard to find and expensive, but they are out there and they can provide you with exactly what you want.
I must just give props to Dimarzio though...I didn't have an email address for them about pups so I just took a shot and mailed
tech@dimarzio.com telling them what I had and what sound I wanted.
They mailed me back within 2 days.
I told them what setup I had...amp, guitar etc... and what sound I was after. I indicated my interest in a certain pickup and they didn't try to sell me on it, they actually said..."well, I don't think that will work with your setup etc...maybe try a blah blah blah because this is what properties it has etc....(they even suggested a product they don't supply)"
Real helpful and great customer service if you ask me.
Made me think they haven't lost sight of the goal...great sounds!
Steve