The Cool Farm Tool uses IPCC Tier 1 method as the basis of its soil carbon module. This method observes that soil carbon stock under annual production is a fixed fraction of the native (pre-agriculture) carbon stock. It also says that changing management practices such as tillage or application of organic inputs to the soil changes 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 with lower native stocks. And this in turn means that if soil carbon stocks (and thus soil organic matter) are higher on Field X than Field Y, then Field X also has more potential gain when changing practices (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. 

The Cool Farm Tool is built for mineral soils (which are primarily composed of inorganic material formed from the weathering of rocks) and livestock globally. They typically have up to 12% soil organic carbon (according to IPCC 2013 Wetlands Supplement) - but this 12% is not a rule for defining a mineral soil. The SOC and N2O models are not suitable for organic soils. See IPCC wetland 2013 guidance and IPCC 2019 definition of organic soil for more information.