See here: Flashlight Optics - Dome, Dedoming and Throw
The luminance of a dedomed LED is higher because of photon recycling. The naked phosphor has a different refractive index compared to the dome made of optical silicone. This also pushes the tint more towards the yellow-green part of the spectrum.
Luminance is important because together with the area of the reflector it determines the actual luminous intensity (throw).
The apparent size of the LED (the magnification of the DIE) does influence the actual size of the hotspot though. This is why the hotspot becomes half the size after de-doming.