I like that the stall mats block moisture from below! And they provide a softer and stable landing when the shavings get moved around (daily) by the birds. Bacteria or whatever on the underside? Actually I don't care, we just clean out the bedding a couple times each year, and rebed with shavings, often a mix of 'regular' and 'fines'.
Chickens live to root around in the dirt and drink out of mud puddles, so having a 'kitchen' level of clean is irrelevant, IMO.
This is no the same a commercial poultry facilities, where 'all in, all out' is the standard, and serious hot spray disinfecting is done between each batch of birds.
Our coop, all wood, would melt or rot away with those procedures!
Biosecurity and luck have kept nasties like Mareks and Mycoplasma diseases out of our flock, may it continue! And if avian influenza hits, the birds are all gone anyway...