Note that different modes of the same scale are only enharmonic in the standard piano tuning (equal temperament). Under different tunings [1], the exact frequencies of the notes in e.g. the A minor scale and the C major scale do not necessarily match up. These different tunings are the reason why certain keys are ascribed a certain character (e.g. the E♭ scale was considered morose whereas the same scale in A was considered uplifting).
Then there's the octatonic scale, the double harmonic scale and quarter-tone intervals present in e.g. arabic music [2], or even more exotic scales [3]. So whatever "deeper logic" you're after, there will always be scales that do not match your preferred system. Be careful you're not straying into numerology, trying to find a deeper "truth" beyond what sounds agreeable to the ears of the listeners.
Then there's the octatonic scale, the double harmonic scale and quarter-tone intervals present in e.g. arabic music [2], or even more exotic scales [3]. So whatever "deeper logic" you're after, there will always be scales that do not match your preferred system. Be careful you're not straying into numerology, trying to find a deeper "truth" beyond what sounds agreeable to the ears of the listeners.
[1] https://en.wikipedia.org/wiki/Musical_tuning#Systems_for_the...
[2] https://en.wikipedia.org/wiki/Quarter_tone_scale
[3] https://en.wikipedia.org/wiki/17_equal_temperament