kepubify is a standalone tool to convert ePubs into Kobo ePubs. It does not depend on any other software such as Calibre, and runs on Windows, macOS, and Linux. It is a command line tool, but on windows, it can be used by dragging the ePub file on to kepubify. It has full support for all the main requirements of a kepub, including Kobo Spans.
 Usage, examples, and FAQ
See the official documentation, as it is updated quite frequently.