One thing I can guarantee you is that you're not losing energy. The boiler will burn the fuel at the correct rate to provide the output power of the STEAM ENGINE. So right now, you're still getting your full fuel value, just at the power (speed) of the steam engine, not the boiler. This is guaranteed because the boiler conserves energy from the fuel into the steam, where energy is converted into temperature and amount, and then converted back to energy in the steam engine from those values. This conservation is only violated by the efficiency numbers, which I've applied, but again I multiplied the fuel values of the fuels themselves by the inverse factor so that you still get the same amount of energy from each fuel item relative to the vanilla game.
Edit: although, come to think of it, you mentioned he is scripting something, so he could be bypassing the energy mechanics. I won't know until I look closer. I'll definitely think about what can be done, though. Happy to take all your suggestions and I appreciate your feedback on my mods.