The migration also doesn't pick up the aliases in Roundcube. The email address for the identities is user@domain.xxx, not the alias.
The set of problems with migrating the email/groupware platform and the remnants of the previous one, in my opinion, don't warrant migrating the production servers.
I think extracting users, passwords, and nicknames and being able to inject them into a clean installation is the appropriate approach, because I see no other solution than restoring a copy of the production servers, changing all passwords to a predefined one, and going user by user, extracting their address books and other groupware applications used, importing them into the clean installation, configuring the identities, etc., and finally applying the exported passwords. Roundcube also doesn't pick up the alias when creating new users.
I'm looking into whether adapting the migratehelper or Lat* script might be the way to go...
In any case, it's a painful operation.