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Well if it is pedantry that we're indulging in here -- when you unzip an epub and edit it using a text editor, you aren't directly editing the file in the epub either.
Your text editor will convert the raw bytes of the file into a set of characters based on what it thinks the character encoding of the file you are editing is. It is these characters that you will edit (unless you are using a hex editor). There is no guarantee that the character encoding your editor uses will be the same as the character encoding any given epub viewer will use for the same file.
Not to mention that if the zip file was created using older/poorly designed zip tools, and it uses non-ascii characters in its filename, it is quite possible that the filenames you get out of the unzip tool will not be the same as the filenames that were put into the epub. Or if you are on windows and the filenames inside the zip file are longer than windows can handle, or they contain characters that are illegal in the filesystem your computer uses and on and on and on...
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