The key point is that biofuel replaces fossil fuel. Meaning, instead of having a system that inputs carbon into the environment, you have a system that recycles carbon already in the environment.
It's impossible to argue against this is a significant and unequivocal improvement.
The points you raised were about corn-based biofuel. Surely you are old enough to hear the comotion about switchgrass, and how it would be the primary crop driving biofuels. I feel like framing biofuels as a corn-based crop is a red herring.
> All of these factors have to be included in lifecycle assessments, (...)
Yes, including those from fossil fuels.