The assumption is not the variation in the nutrient counts, but in the link to obesity.
The rise in obesity has much stronger correlating factors than CO2 levels- diet and sedentary lifestyle being far stronger.
This is especially obvious when looking at the cited study:
> The new study evaluated 18 types of commonly grown rice to see how they would respond to elevated levels of carbon dioxide. In the experiments, the researchers increased ambient carbon dioxide levels to concentrations between 568 and 590 parts per million. Currently, atmospheric carbon dioxide concentrations hover around 410 ppm—but at the rate they’re currently rising, they could reach the high levels used in the study by the end of the century, if action isn’t taken to curb them.
The study examines the behavior at levels of C02 we don't currently have. The decline in nutrients has, thus far, been too small to have the impact on obesity we've already observed.