I would say that you can compare it with the separation of semantic markup and css, the tree structure should reflect the content logic and not the navigation. imagine that one day you want to change the way the content is presented on the webpage... that all the navigation would be rethinked... with this structure, you would have to keep the tree reflecting something that doesn't corresponds to the real situation.
Best, would be to organize the tree by content logic, and make the navigation work as you want on templates.
Personally, I think that a well constructed content structure should make for a good navigational structure and vice versa. Separating them results in bizarre situations like you have in Joomla where articles can be categorized but it has no practical effect on how the site handles the content on the front end. This, in my experience, results in a difficult mental model that frustrates clients to no end. So It seems to me that PW has been developed to eliminate that sort of confusion. When you output your navigation onto the page, you basically spit out the content structure, with maybe some minor adjustments or repetitions here and there, but you're not picking and choosing pages one-by-one and forming a completely different navigational structure. I see this as a strength of PW. And PW makes it very easy to reorganize your content structure, so I don't see that as a concern.
I would be really interested to hear Ryan's take on this.Edit:
understand what you guys are saying--that the separation of navigational elements doesn't necessarily correlate with a difference in the underlying content structure. That being said, if your navigation is well thought out, the links in these navigation sections should
have something in common with each other that makes them fit to be together. In other words, something about their content
should dictate their placement and grouping. So while my previous example fails in that I use a physical page location as my parent item, I could just as easily group these items like so:
And have the children of Cars show up in my main nav with the children of Boats in the footer. In this case, having /cars/ or /boats/ in my URL structure would not be so bad, because it is describing the content.