yeah, that is a dropbox limitation. O'reilly and other sites offer dropbox integration, but they are actually given permission to the entirety of dropbox although they just create a root folder and deposit files normally.
Ehh when integrating with the Dropbox API you're given a choice of "full Dropbox" or "app folder", the latter option creates a folder in your Dropbox which is all your app can access. For an app like this "full Dropbox" is probably more useful (so that you can edit existing files), but in O'Reilly's case it seems they should have chosen "app folder".
Thanks for clarifying... I hope dropbox improves this.