The Mil-Spec boot soles are made of rubber and not PVC/Polyurethane.
The Commercial Spec soles are made of PVC/Polyurethane (injection molded IIRC).
When PVC is burned, toxic fumes are released and this can present a problem in close quarters/confined spaces. I.e. A fire starts inside the hull of a Bradley and a soldier's boot starts burning. A Mil-Spec boot will not be releasing toxic fumes inside such cramped quarters whereas a Com-Spec boot such as an Altama that features a PVC/Polyurethane boot sole, would be releasing toxic fumes.
I know this because I have several pair of combat boots. One was the issued full-leather/rubber sole combat boot. I bought a pair of Altama Mil-Spec Jungle Boots because the issued boots were total junk when it came to traction, comfort, and weight. I had to notch away a lot of the material on the issued boot sole to make it flexible and have better traction in the mud. I still prefer the Panama sole though.