Hm... On the Capitol Corridor they have a "one ticket, one seat" policy. It is in the policies that luggage is not to be stored on the seat. Conductors will sometimes emphasize this by stating if you would like a seat for your luggage you need to pay the rail fare for that seat just as if it were a passenger.

The charge isn't in writing anywhere that I can find but the "One Ticket, One Seat" policy is in the Capitol Corridor Ride Guide and Travel Policies brochure. Not sure how it works on other Amtrak routes but I know the CCJPA sets many of the policies and schedules and administers the route through its offices at BART.