Have you never heard of reproductions? It's not hard at all to take a ROM file, be it legitimate or hacked, and burn it to an EPROM and then solder it onto a compatible SNES PCB. Sure, there may be a bit of technological trickery required for some of the games, but it's still doable.
I consider the in-game engine of FFVI to be one of the best when it comes to 16-bit RPGs, and though it's more out of my personal desire to play, on real hardware, a 'fixed' version of FFVI (ie, no Rage bugs, sketch bug, Evade Bug, proper graphics, etc, etc...), it might inspire others to overcome those very limitations you've mentioned.
You consider the engine to be the best? Despite it being riddled with bugs that you mentioned? If you want an FF6 engine then this SDK is best for you, but there is no point porting it back to the SNES as it will only be played on emulators on machines that can run this SDL already.
If it were easy to back port to the console there would be a load of projects where people have done this, however it is not easy at all, hence why no one does this or even tries to.
It would be a billion times easier for everyone involved if you simply used this software for development and deployment, technology wise it's near impossible to cramp all this into a SNES binary so it will never happen.