I've written a bit about the issues of height restrictions, GPS and barometric altitude measurements. See here.

I propose that it is quite easy to deal with this issue. Competition pilots fly with varios that include barographs. They are recording their pressure altitude. If there is a problem with their GPS altitude, then just review the barograph and see if their barometric pressure altitude recording (which they see displayed on their vario) exceeds the height limits allowed and by how much.

Steve Kroop has already pointed out that the fancy Garmin GPSes (the kind that many pilots fly with) have Flytec baro sensors built in and they are recording the barometric pressure altitude in the GPS altitude field. That should be a bit of a concern to folks discussing this issue.