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The analogy for separating physical file storage and metadata is iTunes. There, you can have all of your mp3's dumped into an arbitrary file structure. iTunes will maintain a database of all the songs, playlists, id3 metadata, scoring and file paths to originals. The advantage is performance, when you are dealing with thousands of entries, large scale modifications of any kind can be much more robust. Calibre will not need to make file moves, or frag the disk space.
For offsite and cloud backup services, it is best not to touch the files too much. One directory rename could end up with your entire library retransmitted over the wire.
Overall, calibre is a very good tool. It has a pretty good support for various formats and devices. I used it with iPhone, iPad and kindle. Once a Book is properly identified (name and title) it is easy to locate and throw onto a device.
As paper book sales giving way to electronic brethren, our libraries will start to grow. The necessity for reliable and non-distractive book management is wanted.
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