Access denied while activating publishing features

Not so long ago I encountered a strange error on a sharepoint configuration: a site collection administrator was getting "Access Denied" errors while trying to activate the publishing site collection features.
As his account had nearly every security right available in that company (way too much) this error was very strange to get.
After some research I tried switching the application pool account of the portal to that of the central administration and apparantly this did the trick.

So the access denied was not received from the actual users account, but from the account the user was elevated to: the identity of the application pool (found in ISS > Application Pools > Your Pool > Properties > Identity).
My guess is that this account did not have enough access to the content databases to perform this action.

Note: This sharepoint configuration was installed by the book of the Microsoft configuration and I've heard other reports of configuration problems when doing this.
I'm no configuration expert so I don't know what right exactly was missing or where in this guide it is going wrong.