Convert the book in calibre. This uses the Kepub Output plugin and puts the book through the full calibre conversion pipeline. The advantage of this is that it can be used to convert from any format that calibre supports and if you have multiple devices the conversion is only needed once. The disadvantage is that it will add the kepub to the calibre library and you can't do much with it there except send it to the device.

Use the KoboTouchExtended driver to transform the book to a kepub when sending it to the device. The advantages are that you don't need to store the kepub, that calibre will convert to epub if you only have some other format in the library and the driver (via the built-in KoboTouch driver) supports other functions such as updating metadata and collections on the device. And, while there are options to do some extra things, it makes the minimum changes needed for a kepub to work. The disadvantage is that it does the work each time the epub is sent to a device (more a concern if you have multiple devices).

Use kepubify to convert the book. (Note: I have never actually used kepubify and my knowledge comes from @geek1011's comments, the support page and looking at the code.) The big advantage is that you don't need calibre and it is reported to be faster. The disadvantage is that for a calibre user, you need to step outside calibre to do something, and you will probably need an extra step or two to achieve the desired result. And you are probably doing the work each time you send the epub is sent to a device (more a concern if you have multiple devices).