im not quite sure what your asking - do you mean more along the lines of - how the tone of the high E you get on the 12th fret of the E has a different tone to the 2nd fret on the D string even though its the same note and your bass has correct intonation..is that what you mean?
Thing is, the notes sound pretty different when you play them on another string, so if you play 5 frets down on the E string and then an open A it wont sound the same even though its the same note.