The frets have to be spaced relative to the bridge - a 24 fret neck will always have a longer fingerboard than a 22 fret neck with equal scale lengths. The idea that there is some sort of magic harmonic at the 24th fret location is nutty. That's actually a node of the string, where it is vibrating least. And of course, as soon as you fret any notes, it's all out the window.
http://en.wikipedia.org/wiki/Node_%28physics%29
However, a pickup further from the bridge will be warmer, as it samples more of the fundamental and proportionately less of the higher harmonics. It's the same as picking closer or further from the bridge, what part of the sting is more "excited." The science of sound is a huge subject. I personally thing that the strong preferences for 21-and-22 fret necks has more to do with the adjustments you can make, the (twanky) tone of a very short string, and, the actually amount of finger space you have between frets. If you have any 24 fret necks you know that the setup is critical to get the strings at the best possible playing height along all the frets, for some reason those last few frets make getting the neck bow right much more finicky. Truss rods generally only come in certain set lengths, so I don't think that they affect the last few frets properly if it's not a truss rod designed for 24 frets and an exact scale length.
Really short strings just don't sound as good, so when you play way up high it only sounds decent if you're in the overdrive category of tone to start with. The 31-fret necks are kind of a gimmick.