I can't actually reproduce this.
I manually inserted an add-on into the DB as follows:
addon_id: OldAddOn
title: Blah
version_string: 1.0.0
version_id: 1
active: 0
is_legacy: 1
Then I created an add-on using the CLI:
addon_id: NewAddOn
title: Blah
version_string: 2.0.0
version_id: 1
(Specified that it supersedes OldAddOn)
All this does is rename the original add-on to have the new add-on ID and version details (which is correct, if you're a developer starting locally, there's no point in making you go through the upgrade process).
Now, I'm not certain if any of the steps I've taken are different, so maybe that will need clarifying, but otherwise the only way I can see this happening is if there was some sort of duplicate entry in the DB, perhaps with slightly different casing on the add-on ID or something like that.