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Short answer: If you're looking in the library folder, you're doing something wrong.
Long answer:
There are three ways to use Calibre.
1. You can use it for library management, in which case you should do everything through the main interface. There's no reason to look in the library folder.
2. Or you can ignore the library management features and use Calibre only for basic processing of your books, such as conversion. In which case your work flow should be: Import into Calibre -> Process -> Save to Disk -> Delete from Calibre. There's no reason to look in the library folder.
3. Or you can use Calibre as a standalone ebook reader. Associate ebook file formats with Calibre's ebook reader, then you can open the books by double-clicking them. There's no reason to look in the library folder.
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