Based on what I read about Valve, it is not surprising that they have a lot of politics going on. That's the issue with flat structures - when authorities and accountabilities are unclear, you need make alliances (seen as "cliques" from the exterior) to get your projects moving forward.

On the contrary, Holacracy has processes that push for clarity. It distinguishes people and their roles, and provides forums (e.g., clear meeting processes) to address misalignments and conflicts between roles, in service of the company's purpose. It's well explained in this 3-min video http://youtu.be/9U_XDin5tjI

Disclosure; I work with HolacracyOne. Hope that clarifies the difference a bit