I like the idea, but I can think of two potential problems. First, versioning. Because of how Aurora gets updated, we'd probably have to rebuild the scenarios with each version.
Second, there are limits to what we can do for specific challenges in the scenarios. You can't set up elaborate AI routines. TheDeadlyShoe's idea about non-NPRs is very clever, but also very limited. So you can't give a near-peer challenge out, and expect the player to have much trouble.
I can see two major uses. First, a tutorial scenario. Start the player off with a reasonable empire, so they can learn how to maneuver ships before they have to figure out how to build them. There's an NPR two systems out, calibrated to be manageable, but not easily.
Second, a case where the player can face down a big NPR. At the moment, NPRs are largely limited to single-system powers, but it should be possible to set up a multi-system NPR with the designer password.