My total custom ft2 skates came in a couple of weeks ago and ive skated in them about 5 times. To be honest im a disappointed in the fit and i think you raise some good points about the scanning. When youre being scanned, your feet are elevated with no weight on them, which is not how your feet will sit in a boot with 190lbs of pressure on them.
I opted to add the 1/4" boot cut to increase the depth which was a big help over the stock ft2 and ft1. I also went with the donut ankle padding. However the donut ankle padding sits too low and therefore the middle part of the donut is not actually around my ankle bone - so the thick part of the padding rubs along my foot and has caused bruising. I also have a hot spot on my right big toe that was not there in the stock ft2. The boot is incredibly tight, i hardly have to tie the laces to feel secure.
For 1299 im not impressed with the fit