Did you have any ports package installed ? If you don't, that might be the reason the system doesn't appear (with your game).
Try installing one of the smaller ports - like lzdoom - this will create the folder and the necessary configuration to show up in EmulationStation.

@shwishblade Well your method works! I just had to install the pixel desktop for retropie from the retropie_setup.sh script (I didn't even know we could install the pixel desktop... neat!). It's a shame indeed that there is no way to run the game outside of play_swing. I also noticed that the game has trouble playing some sounds.

A step in the right direction, let's hope it will be possible in the future!

You'll have to use something like xboxdrv maybe. I haven't gotten around to doing it myself yet.