Connection?
Could it be that the itinerary is not a guaranteed connection (to little time between trains) and thus Amtrak unwilling to chance you making the connection? Is that what you mean by published route? Or are you taking about booking a single train going A- B- C as 2 separate trains first A-B then B-C a few hours later
The way to check is to see if it bookable as a complete trip on Amtrak website.
If it is bookable as a complete trip on Amtrak then it is a guaranteed connection.
Of course you could be looking for a longer layover which I think Amtrak Guest Rewards would allow
Another alternative is to try and book the trip on 2 separate calls.