I believe Vox slightly screwed this up but it's an understandable mistake: the article[1] refers to CO2 equivalent of emissions, not literal CO2. In particular methane from fertilizers seems to have a more negative impact on overall greenhouse gases than whatever CO2 the plants are absorbing.
[1] https://iopscience.iop.org/article/10.1088/1748-9326/acd5e8