The IPCC Tier 1 method, which the Cool Farm Tool uses as the basis of its soil carbon module, observes that soil carbon under annual production is a fixed fraction of the native (pre-agriculture) carbon stock. It also says that management practices such as changing tillage or organic inputs to the soil change the carbon stock by a fixed fraction relative to current stock (the fraction being the amount of carbon stored or released).
This means that soils with a higher native stock tend to still have more carbon under agricultural production than soils which have lower native stocks. And this in turn means that if, after long term agricultural production, soil carbon stocks and thus soil organic matter are higher on Field X than Field Y, then Field X also has more potential gain (as a fraction of a higher carbon stock is bigger than a fraction of a low carbon stock). This is reflected in higher sequestration rates for soils with higher soil organic matter in the tool.
Also, please note that the Cool Farm Tool is only build for soils with soil organic matter (SOM) up to 10%.