So I just noticed that the methane chemical combiner recipe gives a net loss in power, making it completely useless, since apparently methane also cannot be put into boilers anymore.
Not quite. 21000EU cost per Methane Cell and 45000EU gain per Cell (at 100% in a large Turbine) = 24000EU overall gain.
Your Problem is not the Chemical Reactor Recipe, your Problem is your Source of Hydrogen and Carbon, because you are not supposed to use Water to produce Methane.
I can swear you used to able to to use normal chest + 5 aluminium plates in the assembling machine
I could swear I removed the Aluminium Version of the Trapchest->Hopper Recipe aswell.