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.
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Hot: 2001 Estoril M RoadsterZCP 19's michelin supersports, ZHP knob, JL 8W3
Cold: 2002 TiAg M3 6mt
deoranged, dechromed, led tails, ZHP knob, UUC SS v3, GROM, OEM 18's w310's,
Fun: 2006 YZF-R6, black, ohlins, pazzo, cat delete, vance hines csone, YEC racing tune