Minneapolis has two track but lacks the leads so Amtrak will still have stop at St. Paul to drop and add cars.
This seems a little confused. The Minneapolis station is not designed for Amtrak at all. The St. Paul Union Depot has two station tracks, a headshunt, and a siding; it can certainly be used to drop and add cars, and already has been for special occasions such as Boardman's visit. (There's actually room to install four more tracks, as well.)
It is not entirely clear to me why Amtrak has chosen to do routine switching at St Paul Midway, but I suspect it has something to do with being able to use switcher locomotives and crew from the Minnesota Commercial Railway, which would not be possible at Union Depot.
On the whole, most new station plans seem to have a lot of future-proofing. To get back to the topic of Atlanta, both of the Atlanta plans seemed fairly well future-proofed, with one exception: they need to be integrated with MARTA's subway in order to provide effective distribution of passengers.