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I'm not sure what you mean in terms of compatibilty.
You need to be aware that Calibre creates its own directory structure in order to manage the books it catalogs. It first creates folders for each author. Then within the author folder it creates a folder for each book title. When you 'add' a book to calbre it leaves the original book where it is and then creates a new copy and places it in the proper calibre folder hierarchy.
Now, there is nothing special about these folders. Using Windows you can browse to the folders on your computer and see the documents with no problem. However, this means that you can't read the same physical book collection from two different library software programs. Each program would catalog their own set of books. If you need to share a book, then Calibre would copy it from the original place into its directory structure. Furthermore, any changes that affect the physical file would need to occur in two places.
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