I don't know if that truly is the case, but I had an experience recently that has led me to make some subsequent bookings on the website or directly with the airline.

I called into PTS as usual, and I asked to book YYZ-DXB-MLE in EK F which was not showing up on the AMEXTravel site for some reason even though you can see it in matrix, book it with EK and the individual segments showed up when searching separate. The phone agent said they couldn't see it, even when I fed them the flight numbers, which suggests to me that they were not using tooling any better than the website. If they were a proper travel agent they should have been able to price it out.

I had another case around the same time where the agent was super slow and just generally seemed inept. I never ran into these issues in the past.