I've just added all my personal ePubs into Logos. To be honest, it's a bit frustrating having to convert them all into .docx first. Even though I can automate this via Calibre, the results aren't all that pleasing. Certainly, they're nowhere near as good as Vyrso manage with the automated ePub converter you've built for internal use.
Anyway, the suggestion is to put Vyrso's ePub converter into Logos.