Not sure if it is/was just a California regulation, but my understanding was that you can't just buy throughway bus tickets from Amtrak, if there was no train element to the journey?
True, but with a couple of exceptions. The rationale is that it's subsidized service by the state, and it would be unfair to private bus operators.
http://discuss.amtraktrains.com/index.php?/topic/33160-amtrak-book-with-train/?p=469635
Service is provided only for passengers on trips where the
passengers have had prior movement by rail or will have subsequent
movement by rail, evidenced by a combination rail and bus one-way or
roundtrip ticket, or service is also provided on State Highway Route
50 between the City of Sacramento and the City of South Lake Tahoe
and intermediate points or on State Highway Route 5 between the
community of Lebec in Kern County and the City of Santa Clarita for
passengers solely by bus if no other bus service is provided by a
private intercity bus company.
I've been able to book some combinations that don't make much sense but fall within the law. I went down via Capitol Corridor, took Caltrain, then a bus from San Francisco to Emeryville. I could book the bus segment with the early train segment.