[MikeBattaglia]

You are correct. For instance, traditionally, in barbershop vocal music, singers are trained to deliberately deviate from 12 equal, towards an ever-shifting kind of just intonation, in order to maximize the extent to which the voices blend. Auto tune, on the other hand, just tunes things straight to 12 equal. Melodyne fares a little bit better in that it lets you tune to custom microtonal scales, or fudge things a little bit here and there, etc. Interestingly, Logic Pro X has a "Hermode Tuning algorithm" that will basically do the dynamic adjustment toward just intonation for you, but it only works for MIDI instruments and not auto tune as far as I know.