The only way your numbers add up is if (1) Xilinx is losing enormous amounts of money on you
Doubtful. I cant find precise die sizes anywhere, but looking at pictures from various Virtix 6 chips, Im guessing they range somewhere between <200mm and 500m2 (better estimates welcome). At 40nm they arent going to cost xilinx anywhere near those quoted prices to produce them. THe die size and process used match that of typical range from lowend to highend GPU's, and given the nature of FGPA's its almost certainly cheaper to produce them as GPUs (higher yields, due to redudancy, low power etc). List prices may be high, but thats just due to the relatively low volume and high fixed costs.