some might say that foot pain is something we do not need to endure in this day and age.
personally, i still think that despite our technologies, snowboarding still requires you to spend a lot of time on your feet, occasionally slapping and stamping them into the ground and so of course they will ache.
combine that with going on your toes, your heels, and tying up boots and bindings to be at least, very snug, i think pain is inevitable.
my feet never stop hurting whether i be playing hockey, riding the hill or marching around town. its just the way it is.
for you tho, with a new set up, you need time to break your gear in, not to mention for you to adjust to what works best / most comfortable.
so don't stress, just metal up for a while.
Just coz you don't understand it
Doesn't mean it makes no sense!