The difference is that fossil fuels add to the long term store of carbon dioxide in the atmosphere because the carbon released is not a part of the current carbon cycle. Because we’re concerned with the immediate level of CO₂ one source of CO₂ is as bad as any other.

If we weren’t burning any fossil fuels we could burn any amount of fuel from corn or any other vegetation as long as the carbon sinks don’t shrink faster than the sources release the carbon without worrying too much about CC. Living vegetation is a sink, dead and/or burning vegetation is a source.

If we use fossil fuels to create fuel from vegetation then we’re doubling up on our release of carbon => CO₂. The climate system is going to have to come to a new balance eventually but that is going to depend on how large the contents of the carbon cycle gets. That completely depends on how much carbon we transport through time from the past by burning fossil fuels.

Only because we’re desperate to stall the increase of CO₂ in the atmosphere do we consider producing and burning non-fossil fuels as bad as burning fossil fuels.