Eric,
It seems silly for me to charge you for something and then only be able to provide half of the functionality... as mentioned I do not foresee completing ListMail-wide support of duplicates just yet (ie. user editing pages, etc) because I'm in the process of a major interface overhaul as part of 2.0.
We need to have 2 entries in there as that is how we list our accounts
Are you saying you use a script that shows your customers and their domains directly from the ListMail database?
Filtering duplicates on mailing (ie. User Selection) would, I think, eliminate the benefit of being able to use a "message code" to output the users' domain in a message. Therefore, perhaps it is not absolutely essential for the domain to be stored in ListMail.
Custom code can be added to ListMail to run after signup with the included xtra/signup-xtra.php file.
Have you considered an additional table to store domain information linked via ListMail user ID? Any script that reads the users from ListMail could then simply do a second lookup or an SQL join to retrieve the client's domains.
Such a script would take less time (and $) and I can guarantee it will work with future updates.
Regards