Yes, I probably should have added "in equal temperament, ...". I would say that most of music theory assumes equal temperament because it's the simplest to deal with from a theory point of view, because it allows you to modulate to other keys with no restrictions, and because deviating from equal temperament is something that is more of the performer's choice than something the composer dictates. For instance when choirs hold some consonant chords (eg at the end of a cadence sometimes), we tune the notes in just intonation (ie away from equal temperament) to get the nice "ring", and barbershop quartets sing some intervals about one-third of a semitone differently from what equal temperament would be (https://en.wikipedia.org/wiki/Harmonic_seventh_chord), and leading tones are often sharpened quite a lot for melodic purposes; these adjustments are something that you do naturally on a continuous pitch instrument, and composers normally don't specify them.