With an altitude encoder you have no way of knowing if it is out of calibration, and if the aircraft in question does not have a transponder then the pilot may never realise it is out, whereas a GPS can easily report if there is something wrong with the accuracy of its 3D fix.
With better equipment one can monitor the encoder output, and one can always ask ATC what is being seen.
Ask yourself why RVSM isn't predicated on GPS, but on QNE. Nearly everything flying in RVSM has advanced GPS capability. Never the less, altitude isn't based on GPS, even in RVSM, but on barometric altimeter. We do use an air data computer to correct altimeter at altitude, but none the less, it's baro altimeter use, not GPS, and the corrected altitude invariably disagrees with what's found in the GPS.