That sounds similar to how Hubzilla works. Your access is determined by your identity proof, not your handle. This model has been tested for awhile and seems to work well.
The only difference is that Hubzilla will know which one is primary or not, and displays the primary handle next to your posts, regardless of which clone you post from. I think this is important because it provides a consistent handle to people viewing the posts. It also directs any follow requests and direct messages to the primary instance.
That is a good start. They are not truly clones if you don’t move the content as well, but at least it makes migration easy.
One thing to consider is that the GDPR requires data portability, so you probably already have a way to for users to download their own content. If that is the case, the next logical step would be to make it easy to migrate that content to a new clone/instance.