You can set up surcharges / discounts independently in master and referential tariffs. When you create a referential tariff, the surcharges / discounts in the master tariff are not copied to the referential tariff.
See Also
Referential tariffs
List of Surcharges/Discounts for Tariff Charges (Employee)
List of Surcharges/Discounts for Tariff Rates (Employee)