For refrigeration equipment, you should enter the same performance for your baseline as what you are using in the proposed model. There is no explicit way of getting credit for high performance refrigeration equipment in Appendix G (Standard 90.1-2004 thru 90.1-2013).

For some organizations that reference Appendix G, you may be able to make a special request to get credit for refrigeration equipment is higher performance than what is typically installed in buildings. That would be up to the individual organization.

ASHRAE 90.1 deal directly with applications related to occupant comfort. Because the refrigeration system in a refrigerated warehouse is not trying to achieve occupant comfort, 90.1 considers it more of a process load. However, there has been some work done to develop a baseline for refrigerated warehouses by IACSC-IARW. It looks like from this link that GBCI has approved it for LEED as well.