I have solved it!
It looks like it was the difference between using mame2003_libretro.so and mame2003_plus_libretro.so. I had copied mame2003_libretro.so from the regamebox distribution to the retropie distribution by mistake when I was testing to see if that file was the difference in performance... As can be seen above by my documentation of the command which runs the emulator in regamebox, it uses mame2003_plus_libretro.so.
So, to recap, if you are experiencing the usual slowdowns with double dragon while using retropie distribution and would like to eliminate it, you can just copy mame2003_plus_libretro.so from the regamebox distro into retropie wherever mame2003_libretro.so is... and of course have the settings set to use mame2003_libretro.so. Also, i assume if you install the mame2003_plus core and instruct retropie to use it, the effect would probably be the same.
Hope this helps someone out, I know there is lots of talk about laggy double dragon, and there really is no fix because it is emulating lag which was present in the actual hardware of the arcade cabinet... i've seen posts saying to use the bootleg version (ddragonb.zip) because it was built on better hardware, but this looks like a solid and more appropriate approach to fixing it!