The way i understand it BIP16 changes completely the scripting system for the p2sh transactions. How ? bypassing it. Seen lot of code examples already. BIP17 uses an existent placeholder OP code to fit it's needs and another one that seems to have been put there by Satoshi himself.
You understand wrong.
BIP 16 recognizes a certain pattern of bytes, and says "If you see those bytes, then the script will be provided by the person who has the coins instead of the sender (the sender just provides a secure hash of that script)."
The script that is provided is then used EXACTLY as if it was a "normal" sender-provides-the-script transaction.
BIP16 is the most conservative possible solution to the problem we want to solve.