CSR's under some circumstances have the ability to waive fees. It used to be the case that any bookings that could not be done online would be waived IF you asked. Don't assume they will waive them automatically, because they won't.

The IVR message also very clearly says a booking fee may apply, so you don't have grounds to say they haven't advised you.

Having said all of that I've had fees waived numerous times in the past however while booking a trip to the US about a month ago that I could not do online I was told that the inability to do things online did not mean the call centre booking fee would be waived. I ended up just booking tickets online to LAX as the CSR couldn't book the open jaw options I wanted due to lack of UA availability.