Hmm, looks like I was wrong about request depots. I'm not sure what I was doing earlier, but they can fit 100 drones also, or 200 for fluid recipes. So this issue actually applies equally to request depots too, not just buffer depots. So if fuel per drone is >100, then it will overflow the fuel storage amount anytime it refuel back to drone amount * fuel per drone. And I'm not sure about edge cases where the amount of fuel carried per truck causes it to round up even higher than that, so ideally there would be a safety margin above the normal request amount.
The reason that I am trying to use non-default fuel values is that I'm trying to port this to be compatible with my mod, which has limited options for liquid fuel. There is no atmospheric oxygen to combust it with, and it has to be just 1 liquid so oxygen can't be provided separately. To get around that, I'm having the drones be steam powered, but the steam is lower in energy density than vanilla steam or petrol, so it should require a bit more of it.