[itimpi]

At the moment only one format of a particular books can be stored. As for storing files as a "black box" have you tried any other compression schemes (e.g. rar). I do not know whether Calibre looks into those as well.

HTML is put into a ZIP file as it is very rare for an HTMl e-Book to consist of a single file. Normally there are images, stylesheets etc as well. Calibre gathers these all up into the ZIP file. As a by-product you save some space. Calibre has to have built-in ZIP support because ePub books are basically just a ZIP of the contained files. You can always change the extension of an epub book to .zip and then easily open it to look at the contents.