Overriding the main site of a network with a url other than the one set in wp-config.php breaks MU-Migration.
E.g:
wp mu-migration import all site.zip --new_url=http://newdomain.com
If the domain set in wp-config.php for the network is not newdomain.com MU-Migration will not work properly because the main site will become inaccessible by WP-CLI. We should either warn the user about this or try to update the constant in wp-config as a first step.