We usually grind a divot in the heel pocket of the shell in the appropriate position for pump bumps---this relieves all the load on the prominence and still allows you to tighten the ankle buckle to hold the heel back in the shell.
It seems the confusion about your foot width is coming from the way in which you are marking the paper you are standing on ---
you could use a square standing up at the 1st and 5th metatarsal heads to mark how wide your feet are---there is no need to trace the whole foot. Do this weighted and unweighted on the footbed you are using in the ski boots. Give us all the measurements--just curious.