> No, all the carbon in food plants comes from CO2 from the atmosphere.

Yes, this is what I said.

> the natural gas used in making fertilizer is a source of hydrogen and energy, but not a significant source of N.

There is no nitrogen at all in natural gas.

Plants cannot use atmospheric nitrogen on their own. They depend on either bacteria or humans to create some usable form of nitrogen. Any carbon captured in a plant that depended on a fossil fuel source of nitrogen cannot be considered carbon neutral, unless you draw a useless system boundary.