I wonder if this is simply a carryover from OS 9 and before. In the old Apple OS's, closing a window never closed the program, it merely made the window disappear. You had to Quit the application (Cmd-Q or from the menu) to quit the application. Admittedly, there are several OS X apps that quit when you close the main window. System Preferences does (but that's not an application in my book). System Info doesn't quit when you close the window though (would that be "document based?"). However, in the old OS 9 and before, the close window button was on the top right as I recall.
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I wonder if this is simply a carryover from OS 9 and before. In the old Apple OS's, closing a window never closed the program, it merely made the window disappear. You had to Quit the application (Cmd-Q or from the menu) to quit the application. Admittedly, there are several OS X apps that quit when you close the main window. System Preferences does (but that's not an application in my book). System Info doesn't quit when you close the window though (would that be "document based?"). However, in the old OS 9 and before, the close window button was on the top right as I recall.