According to the calculator on co.com the 50% CoS RDM bonus is on 500 mile minimum, not actual miles. The 125% bonus is on actual miles with no minimum.

A flight EWR-DCA (214 miles) in A will earn 750 EQMs, 500 "Base" RDMs, 250 "CoS" RDMs and 268 "Status" RDMs, totaling 1018 RDMs.

Each bonus is calculated against the base number, not stacked like you tried in your example B. Your A is wrong because the CoS bonus has the 500 mile minimum, not BIS.

Hope this helps.