This seems to work fine for me:

This is when the train has one battery being used and one backup loaded, so I don't think it's reading the battery currently being used in those conditions.
The only issue I have is that I can't replace that interrupt with a single condition using the Fuel parameter signal. The parameter needs some fuel in the locomotive to have something to replace the parameter with, and since the train can only hold a single battery, we either have a battery in the locomotive and thus don't need to refuel, or we don't and we don't have a signal to fulfil the interrupt requirements.
Though I guess that's more of an issue with the base game than the mod itself - I'm assuming the interrupt system for fuel was designed to fire when you are running low but still have some, so you'll always fire that interrupt before your locomotive is fully empty. I might need to try and see if it works similarly for vanilla fuels, but I would assume so. If it doesn't, then perhaps something in the way they coded the fuel parameter itself makes it not work properly with those batteries.