Hi John,
For what it's worth, I can't see any logical reason why one setup would be better over another! Essentially we are talking about the left leg, and which way it needs to rock to get certain combinations of pedals and knee levers. I know people have strong opinions on this, but here's my two pennyworth:
The ABC pedals and E and F levers do the same things whichever setup you have, so the same raises/lowers and combinations of these are always possible regardless whether it's Emmons or Day. With that in mind, I believe the Emmons/Day choice is completely separate from any understanding of musical theory, as exactly the same chords can be created through either.
What I think is a lot more relevant is the player's comfort. Buddy Emmons was very tall, and presumably had legs proportional to his height (!), so a simultaneous LKL and RKR (for example) may have felt quite natural to him. For me (much, much shorter than Buddy Emmons) I would find this combination quite uncomfortable.
I've only ever owned guitars with Day setup, and don't even think I've played one with Emmons setup - but I'm happy to stick my flag in the sand and say it really doesn't make any difference to the possibilities when it comes to playing the guitar, it's simply a matter of learning to play with the setup that is on there, or swapping so it's more comfortable.
For a parallel thought process, is there any advantage to driving a LHD car over a RHD car? The controls do the same thing but you use the opposite hand to change gear and work the wipers, etc.!
I shall wait to be gunned down by those who know better...