The new structure of the settings-file allow you to set multiple portals that all link to the same dimension or even 2 obsidian portals

This means:
You can link Overworld with Nether and End (joining Overworld-Portal will link you to first defined travel agent)

or

You can link an Obsidian-Portal between Overworld and Nether and also between The End and another extra World.

Also including new Permissions to allow/disallow creating of portals and joining them -> permission can be set for each portal!