As a (somewhat pedantic) note, MAPt is not always the threshold of the runway.
I can't think of a good example in Australia (since I've yet to fly here commercially, and have only done about 5 RNAV approaches here), but if you check FltPlan dot com, and search Thunder Bay, then navigate to approach plate for RNAV RWY 12, the MAPt (called MAWP in Canadia) is almost 2 miles back from the threshold.
If you're using the GPS for the RNAV waypoints and distance, without also checking the approach plate to see if they match your expectation (please say it is only in VMC you're doing that), that could lead to some pretty low approaches for cases like the airport above. (Why not use the direct to airport, OBS the runway heading trick instead? If you're VFR, and can keep track, you're breaking no rules [that I'm aware of] by doing it, and you get a distance that is within .5 NM of what you want every time)