I think what @drewmccormack is trying to say is that the goal of Agenda is not to become a full-on competitor/replacement for Devonthink, which has a more database-of-all-your-stuff approach. Those apps are often a mix of files and notes, where they are at the same level in terms of hierarchy.
Instead we focus more on the note-taking part where notes can have attachments but attachments can’t be standalone for example. In that sense files are by definition lower in rank than in typical PKM apps perhaps. Agenda can work as a PKM but you’d often use it in combination with files on disk in dropbox, Finder, etc. Or with other apps, for instance like @heyscottyj just talked about in his Nested Folders podcast: Podcast: Actions vs. Reference - Nested Folders Episode 12 - #3 by RosemaryOrchard
So perhaps it’s a matter of definition of what exactly is a PKM, if you think a Devonthink replacement, then Agenda will probably not sway you over, if you see it as a note-taking app, then yes, it certainly can be. And at least for me personally, Agenda is indeed my “Personal Knowledge Management” app, but then again, I have all my files in Dropbox and am not a Devonthink user for example.