Flexibility against Security. This has been a topic for a long time with iOS.
The way I see it, it's more a matter of Flexibility against "Easy Management". I've been supporting softwares for a long time and there is nothing worse than a user who thinks he knows what he is doing. How many times have I heard: I did nothing, it just stopped working...
A file centric system is great when you know what you are doing, I mean, you really know what you are doing. And even then, from time to time, we do a mistake that will brake the system in some way (X11.conf anyone?)
A regular user will eventually spread the files everywhere: On the desktop, in "My Documents" and even on the C: drive at the root... He will install many apps that can handle the same type of file and won't understand why the media player is not VLC anymore but Quicktime... You know the story, after a few months, it's really hard to figure where are the important files for a proper backup.
iOS has taken an approach where the app and the content cannot be separated. For experienced users it can be annoying, but for the regular user, this is a perfect way to keep the damage to a minimum level. And keeping the risk low means easier support, easier maintenance.
On a file centric system, one good way to keep your files organized is to have them in specific folders: Movies in "Videos", music in "Music", documents in "Work", and so on... iOS is not that different as the "Videos" folder is the Movie app and the "Work" folder is Pages. The thing is that the "container" is also the "player". No need to know how to handle the file as the target app will do the job.
Of course, the issue of "flexibility" appeared when more than one app could handle the same file type. Wouldn't it be nice that we could play the movies located in Videos app? But it's like wishing that the movie would be in two different folders at the same time (Yeah, I know, a symlink can be used in Linux to do that). On a file centric system, this would make no sense an would lead to have multiple copies of the same file across the file system.
The app is the "folder", and the player. With the "Open in..." feature, we can also use another app to open the file in some cases which is quite nice. How I wish I could say to my mom: Just look in "Photos", it's there! Most of the time, she has put the file on the desktop, or in some random folder as she wasn't paying attention to what she was doing when asked where to save the picture
A few years ago, the file was dictating the function, now the "container" (AKA Apps in iOS) is doing it...
My 2 cents!