Heck no! First off, I and most other Strat users I know set the bass side noticably lower than the treble. Usually provides more even string-string balance. And the lowest overall s/b the neck, with each a bit higher, bridge highest. Overall, lower heights will put a bit more definition in your sound, but with a commensurate drop in output. Too high, and you'll loose some of those great 'stratty' dynamics, though with higher output. Overall, you just need to play around a bit, as all Strats are a bit different. One caveat, beware of the deaded s/c 'warble'. The strong s/c magnetic pull can produce a funky sound if too close. BTW...the only part of any of my Strat pickup covers that's close to flush, is the base side of the neck pup. Have fun! AC
Start with the bridge pickup pole pieces 1/16th away from the high E string when pressing down at the highest fret. Do this for both the high and low E but drop the low E about 1/32 more. You generally want the bass side lower, it just sounds better, especially once you turn it up a bit. Once you get the bridge pickup dialed in set all the other pickups using the bridge as your reference. Usually all the other pickups will be lower then the bridge but the exact amount is subject to the pickup in the guitar and the individual sound of the guitar.
Seymour Duncan's reference numbers, from what I remember. Pressing down strings at the highest fret.
Bridge 1/16 highE, 1/16 to 3/32 low E
Middle 3/32 to 1/8 high E, 1/8 to 1/4 low E
Neck 1/8 high to 1/4 high E, 1/4 low E
Set too high, pickups can cause a myriad of inexplicable phenomena. Depress all of the strings at the last fret. Using 6" (150 mm) ruler, measure the distance from the bottom of the 1st and 6th strings to top of the pole piece. Rule of thumb-the distance should be greatest at the 6th string - neck pickup position, and closest at the 1st string - bridge pickup position. Follow the measurement guidelines from the chart as starting points. The distance will vary according to the amount of magnetic pull of the pickup.
Bass Side Treble Side
Texas Specials 8/64" (3.6 mm) 6/64" (2.4 mm)
Vintage style 6/64" (2.4 mm) 5/64" (2 mm)
Noiseless Series 8/64" (3.6 mm) 6/64" (2.4 mm)
Standard Single-Coil 5/64" (2 mm) 4/64" (1.6 mm)
Humbuckers 4/64" (1.6 mm) 4/64" (1.6 mm)
Lace Sensors As close as desired (allowing for string vibration)
I bought a used Strat a while back and just couldn't intonate it to save my life. I started to understand why the seller let it go for such a good price - and at the same time think that he had rooked me. To confuse matters further I spoke with some Strat experts locally that weren't so expert. By some surprise I found the tune up instructions on Fender's website. I had to adjust the truss rod, a quarter turn at a time and then measured after letting it sit for 24 hours. After 3 days it was right on the money. Then I followed their instructions for adjusting string height, then pickup height and then went for the intonation. Presto, it tuned up just fine and the warble on the low E was gone. It really does make a difference in intonating if the other stuff isn't done properly first.
My wife and daughter are always telling me to read the instructions...
I've found that setting the pickups very low in the guitars yields the best tone. The bridge pickup I raise a bit, but set them very low and listen. Raise them a little at a time 'til you like what you hear. After all it's what YOU like that matters. I think you get more of the body tone with the pickups set low. Alot of people think strats are too trebly and/or brittle, and they can be if not setup properly. They may not sustain as well but tone will be there with lower pickups. Drive the amp a little harder if needed. By the way, I have been using Texas Specials for 12 years.
Luke, I have to disagree with you. Changing the pickup heights on a Strat changes the intonation and you'll end up in a vicious circle of trying to intonate yet get the right "tone". As you move the pickup(s) closer to the string it has the effect of lengthening them. I know this sounds absurd, but I assure you it slows down the natural vibration of the string and makes it impossible to intonate. You'll simply run out of adjustment room on the saddle(s). If you sink the pickups all the way in it will intonate just fine, but then you'll have no output. You have to find the happy medium where you are in tune and have the right tone. I'm guessing this depends upon the type of pickups you are using and those with stronger magnetic fields will affect this more. String type must also affect this - but its usually a good idea to stick with the same gauge all the time anyway (from my experience).