In my experience (for these types of situations, anyway) if ITA matrix can price it, a TA with GDS access can book it. I am (sort of) a travel agent myself, and have seriously considered switching to a host agency where I can book these fares. It's not frequent enough for it to matter, though, and the commissions are nil, so I haven't bothered. If you can find a TA willing to go through the hassle for you, keep her/him! I've pretty much stopped booking airfare without charging a service fee - and that really only feels acceptable for points bookings.
I suspect these situations arise when something is miscoded in the fare rules - they are not supposed to be available (married segment related) but some error somewhere allows them to technically be patched together. I could be completely wrong, of course, it's just my gut feeling.