Here is how I understand it.GPS sattelites orbit with reference to the center of the earth.that is at a fixed orbital distance.Thus they can pinpoint an a/c position quite accurately in space.But when it comes to the same a/c ht above the earths surface,its only as good as the model of the earth stored in its memory.That happens to be WGS84.Earth not being a perfect sphere does not help either.terestrial gps recievers as used in a car will have a local map of the city stored and position is super imposed on that map.
hence the alttitude discripency.No relevance to change of lat/long