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Emulation Station's button mapping is ONLY for emulation station , not for the emulators that it launches. It took me a while to figure that out.
In the Adafruit guide there is a section under initial setup about retrogame.c that has the button mapping for your device. that maps the GPIO input pins to keyboard button presses.
The emulators are setup to mostly care about the keyboard keys you're emulating by default , but if you want to change the key mapping for a specific emulator, it needs to be done for each emulator either in their individual configuration files, or from the options menu in the emulators themselves. its probably easiest to connect a USB keyboard to your game pi for that configuration and check the retropie fourms for help finding where to change those mappings.