I actually managed to run foul of the 50lbs checked rule this Christmas running CHI-SPG (admittedly some of those gifts were pretty heavy). Boarding in Chicago this wasn't a big deal: the agent at the desk sold me a spacious Amtrak Express box for $5 and I was good to go. It's a great box, actually, and I've held on to it. I don't know if they're set up to do the same thing in some of the smaller stations that do checked baggage.
Another oddity and that I encountered once, and didn't account this time. This summer my wife I traveled SEA-CHI on the Builder, final destination KAL. This was in May so the Devils Lake subdivision was open but there were still various delays. The agent in Seattle refused to let us check our bag, because our final destination didn't have checked baggage service. He wouldn't let us check only to Chicago, even though the train changed there. I thought this was odd. This December, the agent in Springfield had no problem with my checking a bag SPG-CHI, so long as understood what I was doing. I don't know if this a vaunted example of Amtrak's inconsistent customer service, or if there was a temporary policy in place with the Builder to ease connection problems.
Amtrak's thought maybe if you are running late into Chicago, you may have to go right onto your connection. If things are running late maybe there won't be time to pick up your luggage.