Are you sure you aren't talking about the conversion plugin? If this plugin did what you describe, everyone would be unable to properly add Kobo-style books.
As for the conversion plugin, calibre cannot currently support multiple extensions (which is what '.kepub.epub' really is) so I have to use a single extension not in use by any other format. All that aside, the conversion plugin fits quite well into the standard "don't touch the underlying file system structure, let calibre do its job) philosophy; if you use driver plugins that support KePub files to load your device, I could be using '.jshdhjsjeieubbbhhwssjdhhd' extensions and it wouldn't make the slightest difference
If you choose to ignore that for any number of reasons, the conversion plugin will not suit you, and well you clearly already know how to fix the file name to work on the Kobo reader