[un_pogaz]

Even if Kepub is completely spec compliant with ePub, the real issue here is that if you make changes in Sigil, Sigil cannot guarantee that the saved file will be compliant with the strict Kepub formating.
Therefore, it is safer to not allow users to modify a kepub to prevent to broken it.
And I fully understand that Kepub support is more the ressort of in/out plugins.

Else, after thinking about it, the fact that Sigil check the file extension when try to open a file is still quite annoying.
I therefore suggest adding a environement variable that toggle this behavior SIGIL_DISABLE_EXTENSION_CHECK.
If toggle, Sigil will try to open any given file (like in command line), regardless of its extension, and will save the edited file ate the exact same path (so without extension alteration). The target file might not even have an extension that it would be okay.
Since it a environement variable, it a advanced option that only advanced user would use, and toggle it would imply that your on own to open non epub file.