Everything except audio works, including smooth turning, weapon switching & zoom using the encoders.
I have no clue how to send audio to jack, as far as I know, chocolate-doom sends audio like any other standard desktop application…
I was also getting megalomaniacal and tried installing RetroPie (because why not) but ran into several issues.
RetroPie configures many things, there’s probably some clashes with zynthian (although it didn’t break anything from what I can tell)…
The biggest issued seemed to be the X server and permissions, since zynthian uses root for most things and emulationstation doesn’t allow running as root…
EDIT: Audio WORKS!!!
I just followed this guide: How do I route audio to/from generic ALSA-using applications? | JACK Audio Connection Kit
Will post a video of doom running on Zynthian soon, I already completed a bunch of levels ^^
Maybe even make a pull request? 
(the only dependencies are xdotool & chocolate-doom + any .wad game file)