I would imagine that this occurs because some people's skin doesn't slough off as well as others and with the ecezema, dry skin is an issue. The way to keep the buildup and cracking from being a problem is filing the feet. If I don't take a foot file to my feet nearly every day I experience the cracking. There are also products geared specifically toward the feet that help with moisturizer issues. I would focus on trying to make the foot care a fun beauty regimen, big girl stuff she can do for herself, because she is likely going to be coping with this all of her life and it sorta sucks after a while.
I have found that rather than doing the pumice in the bath, if you file them the minute you get out of the tub, it is easier to lose the dead skin and keep that build-up/cracking from happening. The filing is also important from the standpoint that once the heels in particular start cracking, it is virtually impossible to actually make them go away, the best you can do is try to keep it under control and not like those folks you see out and about and wish they had the decency to wear tennis shoes so you wouldn't have to see their dry, cracking mess of their heels, ew.
Everyone is different. My boys tend to get ingrown toenails because they get a calloused skin buildup on their big toes. Never had this with my daughter, just the boys. Sometimes the only thing to do is keep after stuff. With my boys, frequent trimming of the nails helps to skin build-up but I don't think there is a permanent fix for that just like there may not be one for your daughter other than you and she when she is older, being vigilant of foot care.
If this reminds you of her dad, she probably inherited the propensity for her feet to be this way.