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I would expect major differences.
When you copy via Explorer then you are simply copying the files. The actual contents of files are not bheing examined in any way. if you only want to make a backup then this is the way to go.
When you copy via Calibre as well as copying the files related to each book, it is also doing the required inserts into the target metadata database for each book and carrying out checks for duplicates etc and this is a lot of additional work. You can use this feature to guarantee that the target library is valid. The same code is also used to copy books to an existing library where merging needs to rake place.
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