Thank you. This was caused by the environment though. I was booting into PIXEL desktop before launching EmulationStation. This configuration prevents quite a few things to function as expected.
@AEtherScythe after you change the configuration to swap buttons, I believe you also have to remap the controller in emulation station for it to work properly. Hope that helps.
@klachow You can see the version when you start the RetroPie-Setup script.
To get this, you should EmulationStation and then re-configure your gamepad to the joystick axis are added to the input configuration.
For manual installation, you can look at @chipsnblip's instructions.