It looks like BookWithMatrix has now partnered with a travel agency to issue tickets. There is a $15 service fee per ticket but looks as though they will issue whatever ITA spits out (including specified fare classes).
Haven't tried it but seems interesting for some complex itineraries.
Excellent work on their part. The site won't properly recognize Matrix itineraries with train services* but that's a pretty minor edge case. It does work with the UA - Amtrak codeshares though.
* See for example:
https://gist.github.com/nhfruchter/e...546879c4d3b55b