This is not an issue with either mod, rather it's an issue with your refuel stations. Trains in Py work the same way - fuel goes in, ash comes out. You just have to make sure your refuel stations unload spent fuel faster than they load new fuel, so that trains always leave the fuel station with empty output slots.
Although, I will say that from a QOL point of view, that other mod should probably increase the stack size of the spent batteries, or add more output slots. In Py, ash stacks to 1000 (much more than any fuel), so there's always plenty of extra room in the output slots if a train temporarily has too much fuel (for example because the player dumped in extra). Maybe mention that on the other mod's page?