Post count: 4

Ok, @ekdor was spot on. In v3 beta4, a different config file is used. Emulationstation now reads es_input.cfg within a hidden directory (/home/pi/.emulationstation/).

es_input.cfg is in XML format, and appears to call the /opt/retropie/configs/all/retroarch-joypads/*.cfg files. Once I modified these two config files, everything is working now.

Huge thanks to @ekdor and @feederchain!