It’s not exactly number rearranging, even if the government increases subsidy payments to offset the cost. E.g. say gasoline costs twice as much per gallon due to a carbon tax, but subsidies are increased proportionally to offset the cost increase so that food prices remain constant. This still creates an incentive for farmers to use “cleaner” forms of energy as the ones that do will increase their profit margins. Ultimately the increased subsidy is a burden on the tax payer, but in a more narrow sense carbon producing farms would be subsidizing some of the costs for farms that produce less carbon.

Whether this plays out as intended remains to be seen. I think externalities need to be priced in somehow, the issue is determining the appropriate cost. If you want the market to decide the cost efficiently there needs to be some mechanism to tie the two measures together (increased environmental quality => lower carbon tax rate). I agree however that manipulating the economics of food production is dangerous and needs to be done slowly and carefully.