Jason - thanks for your question. I am going to move this to our IC Design community so it will have better visibility to those who are better suited to respond. this community is for general questions or suggestions on the communities themselves.
Are you able to see this TechNote on SupportNet?
It shows a way to use a Tcl script ith DESIGNrev to merge GDS files together and account for clashing of same cell names.
Here's another TechNote showing how to rename cells with a script.
Maybe both techniques could be combined to accomplish what you want?