Hiked 12 miles in the snow last Sunday in "waterproof" Asolo boots. My feet were soaked, but warm. Wouldn't have tried this in anything less insulating.
I think boots are designed to be the shape of feet, so I'm not with your premise. However, it is *difficult* to find boots that truly fit feet that aren't "normal". It is a little easier to find trail runners that fit, or perhaps they are more pliant.
I have had foot problems whenever I have hiked in boots over any real distance. I have switched to runners during this training season. Not a whole lot different, but certainly a lot easier walking. What I've found is that my biggest problems have been almost entirely on the downhill, with toes getting jammed. To that the boots added Achilles blisters on the uphill from the riser.
I'm still not real happy with toe jamming, but adjusting the laces has helped. That's easier to do in runners since the boots are so much stiffer.
Bottom line for me is whether I will be in snow for more than 100 yds (boots) or just among the jagged granite edges (runners). I do not like foot injuries from hard pointy things, nor do I like spending a lot of attention on exactly where I step. However, I often take those shoes right off when I get a chance to walk a forest duff trail, a sandy stretch of lakefront, or even smooth granite.