We're talking about two different choices: fare choice (as you described) and room # choice.
On the travel agent portal, there is no fee charged for choosing a specific room #. or a Guarantee room within the chosen room category.
After the fare type is selected (Advantage, Non-refundable, HIA, etc) for the booking, a list of available room #'s in the chosen room category (not fare) is displayed. The agent chooses a room # from the list, OR checks the Guarantee box, and the booking is complete.
Again, there is no fee for choosing a specific room, or Guaranteed room category from the list.
The selected fare stays the same for either choice.