There are several problems using an external reader
- ibooks does not work offline
- cannot even see epubs in devonthink on iPad
- cannot comment the highlighted passages and search the comments within devonthink
My workaround is to convert epubs to pdf with calibre if I need them in Devonthink BUT the conversion provokes MANY little mistakes, missed letters, breaks, that are annoying when I need to read / quote the texts