I am no expert on this, but I think there are several factors:
1) Laws - restricted ceilings 500ft in USA I think
2) Altitude sensor if there is one, is most likely scaled and therefore its accuracy would diminish as you get higher or lower than the scaling factor.
3) VFR - Pilots eyes, at 500 ft most quads are a dark dot in the sky making it dificult to navigate if you loose orientation
4) FPV - Signal range - I did tests that made it possible to fpv at a max range of 700 feet up and 3300 feet away using futaba 9c 2.4g and 5.8g Vtx in a suburb like setting.
A few years ago I bought a little retail RTF toy heli. At that time I lived in a town whose elevation was 6000 ft. The toy would get even 3" off the ground. I presume it was because of the thin air.
Operating ceiling is a legitimate question.