AlanB, you're probably right about much of what you say. I hope you don't find it combative of me to go point-by-point and comment on your post, though. (If you do, sorry in advance).
It's not a matter of, "can the computer system handle things". It's a matter of who gets how much money from the ticket that Amtrak sells.
If you look at the way Europe works - where most railways are able to sell tickets on any other (and we're talking about many different national carriers, taxes, currencies, classes of accomodations even alphabets), I find this excuse somewhat underwhelming. It may indeed be the source of the problem in the US, but it's really quite a pathetic excuse.
More locally, we also see similar agreements between Amtrak and many bus operators as well as between SEPTA and NJT.
We can't even get the various local NYC transit agencies to play ball with one another by and large, although PATH is an exception. If/when NJT, Metro North, and the LIRR start selling through tickets, then maybe we can expect Amtrak to start doing the same.
I don't imagine this would anywhere near as beneficial (through-ticketing on MTA and NJT services) as through-ticketing on Amtrak to these services. People transferring from Metro-North to NJT are, by and large, frequent riders who know how the system works, know what services are available, know where to buy their tickets etc. If this were any great boon in through-ticketing in commute services, I'd imagine Metro-North and LIRR would have worked this out by now, seeing that they are run by the same entity. Well, who knows, perhaps with ESA, they will be more of an impetus to do so.
Next, it's not one ticket. Amtrak issues two tickets, one for the Amtrak train, one for the NJT train.
Yes, two pieces of paper but only one reservation, only one charge to your credit card, only website to check for timetables.
Finally, with regard to the Boston transfer, all one gets is a ticket that basically says "you must find a way to transfer from South Station to North, or vice versa." The ticket that Amtrak issues when one connects to/from the Downeaster is not valid for any form of transportation within the Boston area, unless there has been a recent change that I haven't read about.
Right, I realize this. I'm just saying that if they don't mind doing this for a passenger travelling from New York to Portland, ME - they could also do it for a passenger travelling from Washington, DC to White Plains. Amtrak doesn't seem to have anything per se against expecting passengers to effect a self-transfer (and well they shouldn't, passengers aren't stupid and if you look at Paris or Moscow or most other major European cities, self-transfers are quite common).