M Ted, you will then (as always with equal temperament) have, if you tune the fretted A on the top E string to the second octave of the fat A string (or the octave of the thin A string) a top open E that is not a perfect harmonic of the open A. What goes around comes around. So many chords use the three-way-unison of the bottom E string, the top E string, and the D string 2 frets up that it makes sense to use the E as your referent not the A. If you are playing in any drop D or DADGAD then the D is a sensible referent.

Another part of the problem is that apart from the saddle that Brian Rodgers built for me with each string (I mean each string, not each course) separately intoned every time you fret an octave course end-effect will mean your strings in that course will be out of tune.