James.
In the limited time I have been a member of the forum you always offer excellent points to ponder and rigorous tech argument to back them up. As we say in Australia, "Good on ya!" I am going to wade back in a bit here and hopefully I wont be toppled mercilessly into the cold water.

Point 1 raised. Hmmm... most 'fanatics' of the Yepes tuning would not agree that even 'well made' 6 string guitars have an even treble response. I have had the luxury of being able to compare side by side two superb hand made guitars on exactly this basis. One a 10 string Yepes tuned and the other a 6 string. Both guitars made at approximately the same time almost side by side by the same luthier using pretty much same materials (probably cut from the same log) and exactly the same body, top and bracing - only the neck, headstock and fingerboard differing. I talk of course about the fine Australian luthier Lance Litchfield. This was not purposeful but the circumstances just perchance happened when he made my 10 string for me late last year and I had access to two of his 6 strings. I have had one of his recent 6 strings here with me for about 2 months as a favour so that prospective purchasers in Sydney can assess the instrument. The rare ideal opportunity for a highly relevant comparison. The 6 string is a very good instrument and I recently had the opportunity of a concert by the superb New Zealand guitarist and educator Prof Mathew Marshall playing a similar model. Sitting at the back of the hall it was the equal of Smallmans in prior concerts by other superb guitarists. In particular the bass response and resonance of the Litchfield was somewhat superior whilst the 3rd string response of the Smallman 3rd string was marginally crisper than the Litchfield. Clearly a fine 6 string instrument and comparable to the best.
Back in my studio playing the 6 and 10 string instruments side by side with the same strings fitted (Goldin on the trebles and Hannabach 200’s on the basses) the difference in the sound (volume, projection, clarity, bass / treble response, resonance etc) of the two instruments hits you square on in no uncertain terms. There is no doubt what "the Yepes fanatics" are on about! As much as I have done the tech analysis and produced resonance map comparisons etc, there is nothing like a side by side comparison actually playing a variety of genres. The difference is certainly marked and complex in that its not just volume or projection but timbre in its truest sense and manifestation. One could get all technical and actually dissect this but in short the difference is significant enough for one to simply concede.
Interestingly I also have the opportunity of comparing different 10 string tunings on the same model Milagro 10 string guitars made by Neris Gonzalez as I have a few of these in stock. Comparing the Yepes tuning with the "Baroque or Romantic" tuning as its commonly called, is also chalk and cheese. The Baroque tuning is similar to the Alto 11 but a minor 3rd lower in pitch. A side by side comparison in this way is really a 'no brainer'(sorry another Aussie expression) playing a wide variety of styles Renaissance to Modern. Overall the Yepes tuning ensures a much more even response and easier attainment of required timbre. However in some pieces particularly Renaissance and Baroque, the ability for added diatonic bass accompaniment is somewhat of an advantage using the Baroque tuning. Personally I don’t like the Baroque 10 string guitar tuning as I think its too uneven with a dissonant mix of deficient and exaggerated sympathetic resonances. It is interesting however (and I have no rigorous reasoning for it other than pure gut feel (no pun intended)) that I absolutely love and relish the Alto 11 tuning just a minor 3rd up. At this pitch it somehow JUST works as a delightful mixture between guitar and lute. The Baroque tuning on 10 string guitar doesn’t! So I love both 10 string Yepes and 11 string Alto with the occasional playing of my beloved 1972 Ramirez 1a 6 string. As an aside somewhat relevant in context and another topic for another day - there is in my opinion a very distinct difference in "the traditional Spanish sound" and the modern powerful "Smallman sound" of a 6 string - both different and both pleasing in different ways without needing to say one is better than the other.
Just as an after-thought, some fellow guitarists when listening to me playing the 10 string reckon there is a difference in its sound as one moves further and further away (back in the audience). The “Yepes tuning” effect as it were seems to decrease the further away one is from the player. Certainly one is very aware up front and playing but it stands to reason as the fuller more complete overtones / harmonics and sympathetic resonances are more subtle than struck notes, the effect will decrease the further away one is. This is aptly backed up when one records and the 10 string Yepes seems to have its own magical reverb without having to add any artificial means.

Points 2 and 3
This is very interesting history. Thank you these insights. Certainly on your point 3 I have found that in our ensemble we have one good fellow that unconsciously insists on plucking notes way up close to the fingerboard when we are tuning to each other. This often results not being able to clearly hear whether he is in-tune with the ref guitar or not. The “out of tune” error is much more difficult to hear than the fuller sound if plucked at the edge of the rosette. It of course stands to reason and supports what you are saying about the distribution of energy across the modes.

Regards, Peter. www.laudarra.com.au.