I've set up the fuel depot being supplied with drone fuel, but when the fuel is actually brought to the rest of the drones it's basically just destroyed? The requester depots only have space for the drones and petroleum. Drone fuel isn't being accepted as something to use as fuel despite being delivered as such.
Am I just missing some configuration somewhere?

if you change the setup settings for the fuel that transport drones use from petrol-gas to drone-fuel it works (for me). try it out to see if it works for you as well :)