Regarding the question of methane or oil: Gas fuels are expensive and difficult to capture and transport. This is why oil refineries burn off gases generated when refining oil.
Regarding the question as to how this process benefits the environment: the article suggests that by processing ALL agricultural byproducts in the US would result in 4 billion barrels worth of energy per year. That would mean 4 billion barrels of carbon-rich oil staying in the ground per year, rather than being released into the biosphere. The process would essentially recycle carbon which plants and animals have drawn out of the biophere.
The process is little more than the application of a little ingenuity to well-established technology. It is neither "bad science," nor particularly high-tech.