The proper way of calculating lux / cd / candlepower

This recent thread brought me back to thinking a bit about this method. As I talked about above, this method seems to make sense, but my measurements disagree with this method of calculating the candela.

I just thought of a thought experiment which makes me further question this method. Say you have a aspheric lens light with an XPL HI. You take aperture and beam size measurements and the calculator linked in the OP tells you the distance behind the lens the light appears to emanate from and you use this to calculate the candela. Now you put a mask right over the LED which decreases its size to 1mmx1mm instead of the original 2mmx2mm. The lux measurement and aperture size stay the same, but the beam diameter decreases by a factor of 2. Now the calculator says the light is emanating from further behind the lens and the calculated candela goes up. But we know the beam candela would not actually change; the center of the LED is left unchanged and so the properties of the center of the beam should also remain unchanged.