Well, the random door thing honestly sounds like an easy fix - not because I know of a technical answer, it just seems socially easy to solve. Have a community project going, like UL, have realms submitted there and vetted. Make one joined mod that adds them all to the random list.
This might leave out a few realms that for whatever reason don't get accepted, but this isn't a problem until there are realms to accept/reject.

Also, it would probably not be too hard to make a patch that links the lot - the accepted realms and whatever realms the user might additionally want - and instructions to do so could be included with the community-vetted version.
Although, I thought Wrye Bash did a good job of merging leveled lists in general, leaving aside the odd interaction. Is there a special reason it doesn't work here?