The main issue is termites. They build mud tunnels up masonry or concrete to reach wood. These tunnels can extend ten to twenty feet. If it is behind foam, it is not visible. Most termite control companies rely on visual inspection to determine the presence of these tunnels to evaluate the efficacy of treatment programs. Makes perfect sense that they wouldn't honor warranties if changes were made that not only prevented them from being able to evaluate the presence of termites, but made an expensive structure possibly more attractive to termites. The seclusion of the foam wouldn't even necessarily force them to construct a mud tunnel. Regular barrier treatments would still work, but they are pricey.
Foam is only good for filling gaps and stopping air flow. It doesn't prevent anything from getting in. Insects can chew through it, and it's absolutely no deterrent to rodents. A trend that I see is people spray foaming attics. They spray the underside of the roof. The downside to this is, if you insulate the top of the ceiling the attic gets warm when the sun shines. This tends to dry things out. If you have a roof, even just installed, it leaks somewhere. It is the nature of screws and nails. Usually not enough to cause problems. But if you coat the bottom of the roof with a six inch layer of foam, every drop of water that ever backs under a shingle and leaks in a nail hole or comes in through a hail dent or a screw that backed out in a wind storm stays right there, on the wood. Have seen some deconstruction projects that point to the big layer of foam on the bottom of a roof being an incredibly bad idea.