In 2.0.10, it looks like a hint was added (SDL_HINT_GAMECONTROLLERCONFIG_FILE) to point to a user chosen 'gamesdbcontroller.txt' file. It looks like PPSSPP doesn't use this mechanism to load the file, but it might affect how SDL2 works when the game controller API is initialized by the emulator.
I'll see if a recent source build for PPSSPP triggers this on a RPi, it could also be something that's changed in the emulator since the last binary build in RetroPie.