How to keep standard cost in make-to-order scenario?

Our company plan to implement make-to-order for all sales. We found that SAP use the value of condition type EK02 to replace the original standard cost in production order GR and issuing. We don't want that because the value of EK02 has little difference with standard cost although we don't know why. How to make EK02 not involving into costing or make them the same value? Your feedback will be highly appreciated.