I think they should find a way to keep the ability to travel to private universes from the live one. similar to how creative worlds work.
Anyone with any technical knowledge can see that portals are the server connection/handshake so its not too far of a stretch to come up with a special portal that allows you to visit a planet in a private universe instead of having to go to one from the client.
I think this would actually be the bridge minecraft doesnt have that makes the live mmo universe feel connected to all the private shards that will exist. that would really take boundless to the next level over minecraft once modding becomes a thing.