Yes, scales are not simply based on the harmonic series. What I would suggest, however, is that their emotional value lies within the rational relationships bet

Yes, scales are not simply based on the harmonic series. What I would suggest, however, is that their emotional value lies within the rational relationships between their frequencies (and I think we agree on this). The physical limitation of instruments with fixed-pitch notes is one reason for the existence of 12TET, but I wouldn't say that it's the main one. The website I linked above gives a good idea as to the mathematical basis of 12TET, and he may go a bit far by calling it "God's temperament", but a logarithmic temperament that has so many close approximations of rational relationships is not just convenient - it's beautiful.