(C) The provisions of Chapter 54, including the provisions of Section 12-54-85, and Chapter 60 of this title are applicable to the fee imposed by this chapter, and, for purposes of applying these chapters, the fee payor is deemed the taxpayer. For purposes of applying Chapter 60, if a clerk of court or register of deeds disagrees with a fee payor as to whether or not a transaction is exempt or as to the amount of the fee due, the fee payor may do one of the following:

1. (1) The fee payor may pay the fee and file a claim for refund request with the department under the provisions of Section 12-60-470. If the department determines that a refund is not due, the fee payor may appeal the matter to the Administrative Law Judge Division. If the department determines that a refund is due, the department shall refund the state portion of the fee and order the county to issue a refund for the county portion of the fee. Refund orders by the department may not be appealed by the county.
2. (2) The fee payor, upon filing an appeal with the department and a copy of the appeal with the clerk of court or register of deeds, may record the deed without payment of the fee. The appeal to the department must be administered in the same manner as appeals of property tax exemptions are administered by the department. If the department determines that the fee is due, the fee payor may appeal the decision to the Administrative Law Judge Division. If the department determines that the fee is not due, the county may not appeal that determination.