The section on stack ranking is really fascinating ... seeing how that sausage was made would let you know exactly who is in the secret cabals the handbook says don't exist ;-)
While there are people who can thrive at Valve, their structure doesn't set people up for success. Valve has a many pseudo-managers, people who have a lot of influence at the company, but aren't designated as such. Doing well at Valve often requires trying to figure out what sort of things these people want, which they often don't make clear. Getting meaningful feedback is difficult, with employees often having little idea on what they need to do differently to improve things.
It really seems like Valve is kind of a mess internally, and they probably wouldn't still be around if it wasn't for the enormous success of Steam.
Your description is exactly what I expected to see out of a "completely flat" company: shadow structures emerging, little fiefdoms run by people who are adept at building and maintaining power, and sheer terror for those underneath.