Well the response there was essentially 'take it to you'. That the entity and all relevant stats are straight from this mod.
The considered response was 'power is basically free from nothing in ATOM anyway'. Which is fair, if slightly inaccurate. Ie. there will be no changes to ATOM and it isn't considered game breaking.
It's not your job to support other mods so if you want to do nothing then that's cool, but I think I could still exploit this with only this mod and the vanilla DLC, and any mod which allows for burning hydrogen for heat or power, hence it is kind of an issue inherent to this mod.
My suggestion is no efficiency modules ever allowed in the thermochemical separator. It already blocks prod modules, or does in ATOM anyway, so this should be easy to code? If there is a code based way to block them from being effected by efficiency from beacons then do that too. Speed modules have a benefit and a drawback, they seem balanced enough to me - they will decrease efficiency, but sometimes you only care about throughput so you may want to use them, as I did, until I realised I can have my cake and eat it too.
Other than that, the only other options I see are remove the module slots, or change nothing and let it be as it is.