Thank you Jacques Vert! I feel like a superstar has just answered my question !! I think the agent thing rings very true. I have now twice added flights to my itinerary through the call centre and neither payment has any logic behind it. The first was more than I had expected and more than what was quoted on the Qantas website for a stand alone award booking. The second booking the agent gave up trying to work out the taxes cost and said she would ring me back, that was two days ago and I haven’t heard back, yet the flight is in my itineraryWelcome to AFF.
When you add to an itinerary (or make changes) the taxes are recalculated. While I have never tried this with an itinerary starting in MNL, there is anecdotal evidence on another thread that those nasty fuel surcharges may reappear. This may depend on whether the agent has to manually calculate the taxes or whether their computer does it for them. @Mattg may have a better idea on this one.
Like everything to do with contacting the call centre, the answer may depend on which agent answers the phone.