If you are a human being, you cannot have a flat foot. Every human foot has 3 main arches to it- medial, transverse, and lateral. What you most likely have is what I have- a very flexible foot that collapses when you apply weight to it. A flexible foot has good arches, just super "soft" ones which allow the foot to collapse and it becomes
flat- it looks flat but is far from it. It has lots of moving parts and needs support in terms of a footbed.
When you place a flexible foot inside a rigid structure like a ski boot, your foot tries to hold on to the bottom of the boot by cupping the flat insole. This is what causes cramps and pain under your foot.
Stretching won't do a lot of good because the problem (most likely) isn't flexibility related. I suggest going to a different shop, one that specializes in boot-fitting and having a real expert examine your footbed needs. There are many different types of footbeds out there and not all work the same. Finding the right footbed is almost as crucial as finding the right ski boot for you.