Well, I'd say that depends. When I play, I am not thinking about what chords or intervals I am hearing. My fingers will go to the major or minor third, for example, because my head knows the sound of what's coming up and my fingers know where to go to achieve that sound. I have very little theory training, but I have a lot of experience playing songs, so my hands know what to do (most of the time) as I navigate through changes, as long as I'm familiar with the music I'm playing to the degree necessary to know what sounds are coming up next. I said sounds because if I said "chords" you'd think I'm thinking Am7 or something, but I never even think about chord names unless I'm looking at charts.
I think that's not a matter of knowing theory or having feel. It's a matter of playing a lot.