How did you actually get the kepub? The Obok plugin should add the book as an epub. It doesn't strip the spans that are in a kepub, but, it will be treated as an epub.
But, you mention "Kobo Plus". Is this a book you have gotten through Kobo Plus rather than a purchase. If so, it is possible that it uses a different DRM, and, it is likely that Obok does not support it.
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