Ok. I don't notice a difference. You can provide me all the evidence that you like. It doesn't change that in my experience, I haven't noticed a difference between difference scale lengths as far as intonation and string tension. I'm not saying that there isn't a difference, but I am saying that I don't notice one, for better or for worse. Playing an instrument is just as much, if not more, about feel as it is science.
And that's your experience. I've always tended to favor thicker strings. I use a 64 on the low B and I tune between B standard and drop Ab. I haven't experienced the intonation issues that you speak of.
Intonation talk is useless without taking into account action height. When I set intonation I measure open, 12th fret and 24th fret. It must have correct pitch on all those frets (even low A). In B-std (0.009->0.054) I have minimal relief and height 1.1mm->1.5mm at 24th fret. With 0.060" at low A (even if the height was bigger due to the nature of the thicker string) it sounded horrible, such a an annoying buzz I just couldn't keep. I don't know it might be corrected with some EQing.
You can't, unless that string buzz doesn't happen to be in the frequency range for your guitar (although I doubt it).
As far as setup, I honestly just set up my guitars so that the strings are as low to the frets as possible without there being any string buzz. When I set intonation, I play an open string and tune it then I play the 12th fret harmonic and set the intonation at the bridge. I don't get into having the strings a certain height above the frets, for better or worse. Once again, I haven't experienced the noticeable intonation issues that you and NjuiMusic speak of. That doesn't mean that they aren't there, but I don't notice them.