Two things- heat dissipation and light center. Most base-up lamps have less distance from the light/heat producing part to the end of the envelope and correspondingly have a longer support structure to the base. When you burn a BU as base-down, the top of the envelope will get hotter and usually fail faster.
An offshoot of that is that the light center may be in a different place, not in the center of the reflector, so the fixture will produce less usable light.