For presence, the extension itself is responsible for updating the state.
I believe they have no effect when using the agent mode.
Well, the PBX is a "stupid" presence agent. We were thinking about making it a smart agent, which calculates the presence state based on registration and calls.
However, the whole presence story so far must be seen as a kind of sales hype; practically nobody used it in the PBX context (AFAIK). In the PBX environment, people look more for BLF and SLA. Maybe Microsoft OCS will change that.