Actually it's worse than that. Per the FAQ, even caches at ground level can be significantly inaccurate where elevation changes significantly. A cache at the foot of a 200m cliff could be up to 200m incorrect. A cache at the top of a pointy mountain will always be lower than the true height of the mountain.
This is just something we have to live with, based on the limits of the technology available. PGC does not want to overide any parameters on a per cache basis as this leads to a HUGE amount of manual upkeep.