But when you weigh out carbon in, say, sodium carbonate, it’s a mixture, and so you should calculate it based on the relative abundance of the two isotopes in your carbonate sample. Except that this ratio varies by source, which is the entire point of the whole exercise. What the exact masses of the pure isotopes is (1) is already known and (2) isn’t what is being changed here.
Actually you should be doing the opposite. The chemical reactions permit you to calculate the relative isotope mixture in the sodium carbonate.