On a shard I play on that is runuo, they have a system called UltimaLive so you can play on more than the standard 5 maps. What if, I changed the batch file for realm generation and uo.em to reflect more realms, and my players download the necessary files, would I have a problem with compatibility issues?

The client only supports the 5 realms. For more you can simply use the shadowrealms available in the 99 core. Which is a copy of the original realms. Check the change log.

The only reason I ask is it appears that Tram and Fel are using the same map, and some ideas I have for both I need to separate them. I was hoping I could do that.