It produces based on how many different item types are in the reactor, so you can take a large amount of low-fuel amount producing items, put them in the reactor, and get more fuel than the sum of their parts. As was mentioned before, Biofuel from the reactor can produce a massive amount of energy with the biofuel generator for MFR (or w/e it was called). However, it burns at the same rate as biofuel from other mods. This said, burning it in the MFR generator makes it produce even more than in a fully heated boiler, but it produces the fuel at 1mb/t. For larger setups, I'd still say other forms of making biofuel will come out ahead due to ease of use, but if you want the most bang for your buck then you'd want several of the reactors and many, many generators (one reactor can feed 4 of the MFR generators with excess, for 64mj/t).
There I go, not rechecking my values and taking what someone else said as fact :O It only produces 160k MJ in a biofuel generator, so using it in a boiler is indeed more efficient.