Pardon me if this is a stupid idea, but why can't you boot UAE with the encrypted ROM and then run transrom on the virtual amiga to get an unencrypted rom? I've never looked at the source for UAE, but it would seem to me to be a huge slowdown to unecrypt the ROM as you run the routines in it, so UAE probably just unencrypts it on bootup, and the virtual Amiga just sees it as a regular, unencrypted chunk of data (which you can just save off with transrom).
