This link is to a very neat fret spacing calculator that I've used myself. It's small, accurate, if you're into this kinda thing, something you shouldn't be without.
http://www.hitsquad.com/smm/programs/Fretspecs/
Dave, at first glance, it may seem that some of the variables you've mentioned would have an effect on fret spacing but it just ain't so. Given a standard scale length, say 34" as in the Fender, the basic length of the scale is 34" (with adjustments made for for intonation) but the 12th fret (primary harmonic) is exactly 17" from the nut. That won't vary at all until you change the scale length. Fret height doesn't change spacing or intonation either since the string doesn't know (or care) how high the fret is. Besides, when you play, you don't actually press the string down all the way to the fretboard behind the fret. All you actually do is press hard enough to stop the string from vibrating. It actually takes only a bit more pressure to fret a note than it does to create a harmonic on an open string. String height CAN have an affect on intonation but it would have to be an extraordinarily high action to begin to hear the difference. But your observation isn't without merit. You've actually pointed out the problem with fretted instruments and their relation to the scales we are used to hearing in western music. In reality, our instruments aren't perfectly "in tune" no matter what we do to make'em that way. Of course this is a matter of small degrees and, over time, we have come to hear the fretted bass as being in tune. This is also a very technical subject and one that I'm not very well versed in. If you want a real long-hair discussion on this subject search the Bottom Line (a subscriber digest for bassists). I seem to recall that there are several threads that elaborate in great detail on this subject.
