I love my corporate TA. Currently, they will only book HBO fares in Europe on BA and then charge me for bags on top. When I pointed out that it made them £40 more expensive than booking with BA direct and for a non-flexible ticket they told me that I probably wasn't looking at the right fare on the BA site. I'm sure that's correct. It's not like the same company is unable to find fares in Premium Economy on anything but routes served directly by BA and Virgin. They excitedly rang me once to say that after I had complained they had indeed found a Premium Economy fare to my destination.
"But Air France don't fly to Dhaka" I said.
"Yes they do, I've found a flight via Paris".
"That's Dakar in Senegal" I replied, slightly irritated.
"Does that matter?" was the reply
Back to the OP. Do you know how much the same (refundable) fare would have been had you booked direct? Only if I was sure that the CFO was receptive to a money saving approach from a new member of staff would I go ahead and do so. Thankfully mine is.