Actually, you understand the issue just fine. What you have to do is suspend logic for the duration of your Amtrak booking.

Trains 7, 27, and 807 between Chicago and Columbus (WI) are all the same train but are portions of the train. Train 807 is the coach(s) that only goes as far as Minneapolis. Train 7 is the portion of the train that splits off at Spokane and goes to Seattle. Train 27 is the portion of the train that splits at Spokane and goes to Portland. Now, here's the neat part. Amtrak's booking system thinks these are really three trains and sets separate fare buckets for each. So as Train 807's seats sell, the price goes up. But if lower bucket seats are open on 7 and 27, the price is lower. Same train physicly, different trains in the booking system, different prices.

Bottom line: book the lowest price.