I use a mid sized, TA in Melbourne that probably mostly looks after mid sized to small corporates, but also lots of individuals (like me).
Not like Flight Centre, and I don't think FC will give you service such as the below, unless you are an established client (but I'm only guessing about FC).
I believe their main transaction system is 'GDS' or Global Distribution System. Most mainstream hotels, tours etc are on their GDS, but not all. I understand that when they book through GDS, they automatically get credited with their commission. In my experience, the price of a hotel or flight booked through my TA is about the same as what I could get doing it myself. Sometimes a bit cheaper, sometimes a bit dearer. But I give it to the TA as they spend their time sorting things out, giving me options, foreseeing issues etc. For flights, they will use the Amadeus or Galileo booking engines, and again, take their commission from the airlines. They have a direct line to airline reps, so can ask about anomalies, availabilities and 'rules'.
When a hotel isn't on the GDS my TA just tells me, sometimes suggesting I might book it myself, but other times booking it through the hotel web site or Expedia etc for me. If they do this for a corporate, they will charge a booking fee, as they won't be earning commission. The only hassle I've had is from Accor, whose hotels sometimes think a TA booking doesn't earn points, as I'm not the one paying. But I point out that all the TA has done is use my cc, and then its all sweet.
TAs have access to tour 'wholesalers' who can stitch together a custom tour etc, which may not be apparent on any web site.
How much cheaper are they likely to be able to do as an employee benefit compared to what the average non-AFF traveler will be able to find with minimal effort? I assume all they'd be likely to do is perhaps waive the agency commission they receive from the airlines?
Not sure what you mean here. You can't expect them to waive their commission ... AFFers may be able to get fares cheaper via various investigations, but on the other hand, my TA lets me know of various airline deals sometimes not available by simple inspection of the web site. And again, as long as I get a decent fare, I'm happy for the TA to book it, as they then look after any changes / re-bookings and (for instance) can roll-forward bookings, thus putting off the time when payment is needed. My TA looks after seats, keeping an eye on availability etc etc.
Bottom line - many here have the knowledge to get great deals themselves, and enjoy the process so do well without a TA. I enjoy the planning, and research, then hand it over to the TA to book, anything, worldwide, as I don't have the time or patience to do the mechanics.
Hope that helps.