I have never heard of being able to set the IPCC extension outside of Call manager. Even if you could, someone would still have to go into the RmCm admin account to add the device. And there's no way PCP would be able to do that. In my environment, the people using Provisioning create the phones/lines then tell the engineers the user ID, which extension is the agents and they go from there. Whoever is associating the agent with the CSQ should likely configure them as agents.
I appreciate what you are saying, however It is very annoying when the workflow that manages the users and endpoints in PCP has no ability to just make two additional changes that would alleviate "the engineers" from having to go back and perform a mindless task. This is a glaring oversight in PCP that needs to be resolved.
I was just looking under Infrastructure configuration from PCP, and it looks like there is a section to update the RMCM admin account with agent devices as well as end user configuration. I'm curious if you have any luck with this, as I'm unable to open Call Manager from PCP. I receive a timeout error every time I try.