Yes, the travel agent we use basically always gets us lower fares and is patient and wonderful at answering questions.
As for one of the others you mentioned, for one of our cruises we booked a flight with the first one you mentioned. And then the airline changed the flight from direct to Fort Lauderdale to a stopover in Dallas. We might have got to Fort Lauderdale in time to wave goodbye to the cruise. A real TA would have done something, but they just basically said tough luck. (We did get the flight cancelled and used a different airline by calling the airline). And this, as you pointed out not a real TA, charged us (IIRC $15) for the service of booking a flight that became unworkable.