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In my humble opinion, the benefits of moving all content to one location far out-weighs the benefits of leaving content where it was and adding those locations to the database.
By having all content in one location it means that backups / transfers to a different computer or even O/S are trivial matters; you only have to worry about the directory tree that contains the metadata.db.
On the other hand, books being left in their original locations would mean that not only would I have to backup / transfer the metadata.db and it's directory structure, I'd also have to track down each and every book on my system, and ensure they were backed-up / transferred, I'd also have to hope and pray I could use the same directory name as that file was initially in. No hope at all of moving from say Windows to OS/X or Linux, and even on a Windows to Windows move, I'd better hope that the folder for my Desktop was in the same locale.
Also, by leaving items where they originally were, you're now opening yourself to the original location being managed by some other program, and those files being moved to where calibre was not expecting them to go.
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