The fossil base is the heating aspect, and maybe if they are including it, is the fuels used on the farms. If they use the methane for heating, then that lowers the petroleum usage. Natural gas is what is used typically, as it is readily available Last I knew, natural gas isn't at much risk of running out, but that still is no excuse, if they can get the heat from natural sources, other than petroleum, it would be better. There are some as well that are taking the stalks and such for burning. Initially, ethanol is using natural gass, but in time, they likely will move away from it.
The one thing about ANY alternative fuel is that it takes time to figure out how to produce it, as well as use it. If we are truly going to move away from petrofuels, the engines will also have to as well, or however the power source. We simply will not be able to just keep using the exact same engine, and expect all the fuels to work in them. It takes time and money to build the infrastructure, and if we all just wait for it to be there, it won't happen.