When migrating visitor cookies it is often required to migrate from multiple 3rd-party tracking domains (e.g. track.mysite.com and track.mysite.co.uk and track.mysite.org) to the new first-party tracking domain (e.g. track.mynewsite.com).
The old, script-based method for handling visitor migration allowed you to do this easily, but the new server-side method, where Adobe do the configuration for you, does not allow this. Instead, at best, numerous sub-sub domains must be set up, with associated secure server certificates (e.g. track.track.mynewsite.com) which is a backward step and difficult to manage.
The server-side migration process should easily allow you to simultaneously migrate from multiple tracking domains into a single new tracking domain.