Hey there, I'm glad you like the mod. The charging code only recognises the mod's own locomotive entity. It would be fairly simple to modify; if you want to test it out, modify line 100 in my control.lua to read:
if w.name == "electric-locomotive" or w.name == "electric-locomotive-mu" then
It looks like the fuel balancing code should be okay, but the train replacement code might cause issues, if a change happens while mine's in the process of recharging. I do redundant checks as failsafes so I think it will fail gracefully and remove orphaned entities, but who knows.
Edit: It occurs to me that you probably know all that already. I can probably make my mod more flexible too, so that it can play more nicely with yours and any others out there that want to add variants or use my charging mechanics (unlikely as that may be). I'd be interested in doing that, sure, though I think it might take some significant restructuring of mine.