I'm not sure.

GPS systems (all mapping systems) make assumptions about the the shape of the earth's surface. They generally assume that the surface is "smooth". Each system uses a different "geoid". And the differences while small can have an impact.

I've done a lot of blue water sailing -- there have been may times when a GPS unit has shown me at 150 feet above or even below mean sea level. (An aside, GPS is a very bad thing for coastal navigation -- one's eyes and a knowledge of how to use a chart are far better...)

But, +/- a few hundred feet should not be a problem at 29,000 feet. At the height that airliners are spending most of their time they should be OK.

But if east bound and west bound flights are supposed to keep 1,000 feet of vertical separation this could easily eat into that.