I'm not all that familiar with actor migration, so i might be misinterpreting.
We've recently had some complaints on project:support_desk ( https://www.mediawiki.org/w/index.php?title=Topic:V6ka95f08v2c89yp ) about stuff going missing on upgrade involving users with id 0. I think the issue is that update.php doesn't run cleanupUsersWithNoId.php prior to running migrateActors.php. At a glance, I don't see why we wouldn't do this.
When run manually, you can decide whether users with 0 ID but a locally existing name should be merged into the local user, and what interwiki prefix should be used for non-merged users.
I guess selecting no / some unique prefix like migrated is non-destructive so the automated migration could do that, but it would then be nice if the user could manually change those choices later (ie. tell the migration script to merge all migrated>... users into the local equivalent and/or change the prefix name, which is sometimes used as an actual interwiki prefix when linking the the user).