I got the non-libretro version working for pi zero (Retroflag Gpi case) and wrote up a guide in case it helps anyone interested in Cannonball on Pi zero: https://sinisterspatula.github.io/SuperRetropieGuides/cannonball and also, if it helps retropie dev's in adding a pi zero specific version, my modified repository that worked for zero is located here: https://github.com/SinisterSpatula/cannonball