The Depot is owned by the Museum and connected to it. To be honest, the Intermodal Facility is more about having a parking ramp in the millwork district than it is the actual train. The train ironically might not even stop here because of issues the city is having with CP over the trackage.
Probably not, but the Empire Builder did originally run on the Great Northern Tracks that BNSF now owns pre-Amtrak was was routed through East Dubuque and Prairie du Chien. When Amtrak took over the route, they moved it over to the Milwaukee road tracks used by the Twin Cities Hiawatha.