House Edge
House edge is determined by the rules alone (# of decks are part of rules). The house edge is based on a freshly shuffled deck. As cards come out, the edge changes. Counting does not affect the house edge. Counting gives the player the ability to realize what the house edge (or player edge) is at any given moment. The edge is directly related to the count.
Your example of casino A and B would yield the same "house edge" because the rules are the same.
Penetration affects something called desirability. The only real way to determine a game's desirability is to run a simulation with all game parameters defined. Including aspects of your game (count system, indicies, bet patterns). You could run these sims all day changing only penetration, you will realize that the more penetration you get, the better the game (you already knew that).
So the long and short of it: If you have the opportunity to play at two casinos whose rules are the same, but one deals deeper, play at the casino that deals deeper. If you want to know how much you will earn per hour because of that penetration, you need to sim it.
