A tuner has fixed frequencies, like a piano or keyboard. That is fine if we are tuning a piano where we are forced to comprimise. When playing instruments without fixed pitch, we have to "bend" the pitch to get the optimal intonation (generally least beats). Except for octaves, every note needs to be adjusted. The frequency of a A is different if it is in an A major, D Major, B7 or F Major chord. Tuners don't know that and that is why they are not really optimal for real life playing. I am pretty sure that it is not even possible to memorize the frequency for recall in ensemble playing. My experience is that we develop an ear for the "color" of the chord, or minimizing the beats that occur when out of tune.