What a good question.
I did nearly 400nm round trip today and was comparing the GPS altitude(twin IFR certified Garmin 430s) with the altimeter (as well as a few other things). It wasnt totally scientific but IO540 is correct, the differences were very small indeed.
430s must report a RAIM error when the function is unavailable but without a RAIM error what tolerances of vertical nav. should be expected and what tolerances are assured (if any). I must do a little research when I have a sec unless anyoen knows the answers.
To answer the question if for any reason I couldnt set a pressure (I cant think why that would be so mind you) I would definetely use the GPS height to calibrate the altimeter and if the GPS height and altimeter were at variance I would definetely want to estabish why.