It doesn't make any difference whether they are using biofuel or not in the machinery.
Suppose that a hectare of land can produce 10 tons of oil equivalent per annum via either fermentation or some thermochemical process. And suppose that 1 ton of fuel is used in the process of growing and refining the feedstock. Then there is a net production of 9 tons of zero net carbon dioxide emitting fuel. Whether the one ton for the process comes from the process itself or from fossil fuels matters not one whit.
Of course, if it takes 11 tons of fuel to produce 10 tons of oil, then we have an energy sink, not an energy source.
David F Mayer