You are right on the GST and probably the transportation doesn't count either, but it might. One thing you have to keep in mind is that anywhere from 4.5% to 5.5% of your bill are a variety of fees; Sydney Harbour Marriott charges 1.5%, Visa standard FX fee is 3% and then the issuing bank of the CC may add 0.5-1%.

FWIW, my stay this past December at the Sydney Marriott came out just fine point wise, and did not have any transportation charged to my bill.

Now I have run into blatant short changes on stays, but IMO MR is not to blame. The blame rests on the individual Hotels as they submit the eligible charges to Marriott Rewards for posting and they pay for the points. There is no motive for MR to short change anyone.

My bet is that transportation is a "Paid Out" and as such are charges that do not qualify for points earning per MR T&C.

If you think you are short changed, then call MR and have them check it out adn be prepared to FAX them the folio form the stay in question. I have done this a number of times. About 50% of the time they have been easily explained and other times the points were corrected. FWIW I have experienced this much less in recent years (and actually been traveling more internationally), than I did 5-10 years ago.