Indeed commercial tools like Scrivener comes with ample warnings about what it can and cannot do. So all software comes with limitations. But it is the case that when something doesn't work right in Bookends or Scrivener, I bug Jon or Keith, and they will fix it or tell me of an alternative route to do what I want. There really is something to be said about a well supported program from a dedicated and passionate developer & support team.
The salient point is not whether it is open source or commercial, it is actually the support provided to make it a working tool. Some open source projects like FireFox go to a lot of effort to make it work. While some commercial products seem like they find customers to be a nuisance. One commercial product that gets rave reviews from its customers is this creator of Dreamweaver extentions http://projectseven.com. I am one of their very satisfied customers.
Anyway, now to test drive BookEnds.