Check allowance sets the distance that the tools will approach, but not pass closer than for a check surface. If Check allowance is set to a specific value, that value is used for both rough and finish passes. If it is left blank then if behaves differently for roughing and finishing. If left blank for a roughing pass then check allowance is set to finish allowance + leave allowance. If left blank for a finishing pass then check allowance is set to leave allowance.
More information about check surfaces.