All of this. This is why cesarian births aren't optimal for the overall health of the baby. I did read somewhere about how one doctor was trying to remedy that situation by doing a quick swipe of birthing muck inside newborn nostrils and mouths when they are born cesarean. I don't remember if anything came of that though or if he proceeded to a testing phase etc.

I think that may be due to prolonged exposure. Because our bodies attempt to attain homeostasis constantly, our bugs will naturally get rid of a small introduction to something foreign. But if it's a constant input of something foreign it attempts to reach an equilibrium without having to constantly rid itself of foreign bugs.