just running a motor too lean can, and will eventually damage it even without knocking. But just for a reference point for you.
My motor is a m52b28, pretty much stock. I'm running s52b32 software on it (litterally, took the chip out of a M3, put it in my car, no tuning).
Because of things like the Maf, CPS, O2 sensors, etc, your chip makes sure its running correctly. You can usually tell a poorly tuned car very quickly. Like mark has said, dont worry about it, put the chip in (assuming its for the correct motor (vanon vs-non vanos) and enjoy.