From your description of the missed connection debacle, it sounds things have changed, perhaps due to their becoming routine.
The two time we missed connections (EB both times of course), our hotel was close by. The first time when we arrived at 1:00 AM, we skipped the ticket line because we had received the vouchers from a rep put on the train at Wisc Dells, and knew we could handle the ticket counter part of it the next day. We headed straight to the hotel on foot, and pocketed the cab (no bus) fare.
The second time we were able to bike to the hotel and again pocketed the cab fare.
Both hotels were used to house Amtrak OBS personnel. The first was a somewhat downscale Roadway Inn only a few blocks away; and the second was the very nice Inn of Chicago on Michigan Av's near north side. Being herded onto a bus to the burbs is definitely a downgrade in my book.