Fascinating stuff. I would love to read a follow-up that covers hybrid systems in depth, as that’s an issue that many site owners confront every day.
As a manager of (lots and lots of) content, I struggle with this daily. In fact, there’s something deliciously meta about this article being listed under the PHP section when it has very little to do with PHP! I suspect it has to do with editorial assignment (and @swader can chime in), as you describe in the Tree section.
It becomes messy when you factor in multiple platforms: content that “lives” in one CMS (let’s say WordPress) will be distributed via many channels (RSS feeds, either via a full feed, a category feed, or a tag feed), found via search engines, and, in our case, listed on a forum with similar categories.