How does "breathable" siloxane water sealant work?
According to How silicone water repellents work, 
"Because silicones have a very open molecular structure, water vapor trapped in the substrate can easily slip through. Water molecules, however, are too large to enter."

If I remember correctly, siloxanes' Si-O bonds are not intrinsically hydrophobic, but the long molecular chains with outward-facing hydrophobic methyl groups, and thermal molecular motion, prevent liquid water from seeping through, which presents less of a barrier to water vapor and other low-molecular-weight gases.