This was a question i thought about myself before.
I dont think it is possible to get perfect intonation on a guitar unless you press down on each string with the same pressure each time. I suppose if you used a capo on the 12th fret and tried to intonate it, you could probably get it pretty close. The capo giving you consistency each time you apply it to the twelth fret. But for me, every time i push down the string, i know it isnt with the same pressure as the last time no matter how hard i try(maybe a little more, maybe a little less). And i certainly dont press down as hard as a capo when i play.
I have a Seiko Tuner (your average $20 tuner), and when i intonate, i try to get it within +/- 4. Anything more, and my ears can sense it just starting to go a little sharp or flat.
I think the key is to get it close, knowing it wont be perfect. It's gonna be better than if you werent to intonate at all (and i'm sure we've heard how bad it sounds on a guitar that needed intonation real bad).
Dana