As a travel agent I must say I absolutely agree that this "late fee" is a ridiculous insult from the tour operators (- NOT the travel agent ).
I have never understood why ,when tour operators are desperate to get rid of those last seats they ,on the one hand ,reduce the price, and then on the other hand add this fee.
Your travel agent should have just quoted the total total amount. full stop. However, she may have faced the problem that we all face which is ..
The tour operator (or airline) advertises this great holiday/flight for only XYZEuros.
Client comes in - she wants that holiday/flight she saw advertised.
Then we have to explain that ,yes, the basic price was 369 but the tour operator is adding late fee -oh, and airport tax or departure tax whatever blah blah blah ETC
Very annoying.