FWIW, my teach/luthier tunes by ear as well. He tunes to one string and then plays up and down the neck to play around with compensating for fixed temperment. One day I'll have him show me how. He'll tune my guitar to his one string and then goes thru his ritual...he's quick about it and the guitar always sounds great when he does it.
For setups and intonation, though, he uses his well-worn Conn Strobotuner.