OK, so after some quick scanning I have some good and bad news
Bad news
Annoyingly, due to what moorings are in the code (proxy containers), there doesn't appear to be any way to target both the fuel and burnt fuel slots at the same time (Nuclear reactors allow you to target both at the same time, but again, this appear to not work with proxy containers)
Good news
I can think of a few workarounds
- The first and most obvious solution is to add a new mooring for burnt fuel. I'm not too fond of this since that would add even more mooring spam
- Add a different area on the mooring that specifically targets the burnt fuel slots. As an example of what I mean: the 3 tiles on the right side of the mooring allow you to access the burnt fuel slots, whereas all the other tiles would gives you access to the fuel slots
- While at the refueler, have the drone check if it has any burnt fuel, if so; have the mooring target those slots first. Once those slots are empty, switch to the fuel slots. This has a problem though, which is that anything can be put into the burnt fuel slots, so inserters pointing into the mooring would start putting fuel into the burnt fuel slots. The solution to that problem would be to have the mooring output a circuit signal based on what slots it's targeting, allow us to turn inserters on/off as needed. Making this rather complex to use, but easy to implement
Likely I'll go with the last option for now, since it's the fastest to do. But I might change it later
I would welcome other opinions and ideas though