This is where all the controller files generated by retroarch joyconfig tool are kept, they are effectively the auto files and can be used on a hot swap basis:
/opt/retropie/emulators/retroarch/configs/

This file is always used by retroarch emulation regardless of your controller, so settings in here would be effectivly hard coded and always run.
/opt/retropie/configs/all/retroarch.cfg

There is no significance of the fact that some of the controller files are set to be executable.

This should help more:
http://www.dailymotion.com/playlist/x3nvkw_smartretro_retropie-usb-controllers/1#video=x2hudlt