I Know That The Distance Between The Strings and Pickups on my Strat Can Significantly Affect Tone and Intonation -- What's the Best Setup?

It would be hard to design a pickup with more flaws than a Fender Strat
pickup; high impedence, noisy, low output, no bass response, microphonic,
and all this with magnets strong enough to pull the strings out of tune.
But they sound cool.

The usual practice is to lower the neck pickup on a Strat until you can
tolerate the 'out-of tune' sound on the bass strings, and adjust the
other pickups a bit closer, and try to get the overall volume similar,
which usually means lowering the bass side of the pickup further,
especially the neck pickup.Bridge pickups are often closer to level.
But most new pickups can sound more harsh, or edgy, (strong
upper-midrange) when adjusted close to the strings, particularly the
bridge pickup. It's a question of finding a lower adjustment
height that works for you.

One problem is that lowering the pickups increases the relative noise
level. Think about it; lowering the pickup lowers it's output, but not
it's noise leve, so the signal to noise ratio 'disimproves' as you
lower the pickup.

'Some' brands can be adjusted very close without problems, and get
rave reviews for being very quiet. Old pickups, aged magnets, and more efficient pickup designs (like mine) often have a wider range of useful adjustment, without producing undesirable effects, and allow the final setting to be more a matter of personal taste.

Lowering my V+ Tele is usually a less agressive, kinder, gentler
tone, more country than blues, but then the amp settings can make
the cleaner twangier tone better for blues anyway.