My workaround:
Short Answer:
Convert the [none-DRM] epub to a pdf using e.g. onlineconverter
https://www.onlineconverter.com/epub-to-pdf
Import into Bookends
Proceed as for pdfs.
Longer Answer:
I've consumed some time on this and perhaps providing a note may save others doing the same!
I understand why Jon wouldn't want to spend time on this. But I also end up with occasional epubs, usually books, that I want to annotate as part of my usual workflow (Which is Bookends for managing pdfs and making notes; Devonthink for dredging up related papers, including those that I gathered years ago, using its fantastic concordance feature. In Devonthink I can also see pdf highlights and notes made in Bookends (or elsewhere); Tinderbox for working up ideas now including links to text highlights made in Bookends (thx Jon!); Scrivener for writing, including refs from Bookends).
The following comments are about epubs that can be opened in Calibre - i.e no DRM digital rights management.
You can highlight and make notes on ePubs in Calibre, but they are pretty much stuck there. If you put a copy of the ePub into your Bookends folder and click on it in Bookends, Calibre immediately imports a copy into the Calibre library, which means you end up with multiple copies there
Epubs in your Calibre library folder can all be sucked up and indexed in Devonthink (so if you open the epub you can see all the epubs and pdfs that are related to it using the concordance feature) but the comments and notes are not picked up- so this is not a viable option for my workflow.
So I convert the epubs into pdfs and import the pdfs into Bookends.
HOWEVER - there is an issue between Calibre pdf conversion and Bookends (at least). This happens both with the simple 'print' command from Calibre and outputting to pdf, and with the sophisticated 'Convert' Book module in Calibre.
The issue is that when the pdf created within Calibre is imported, opened in Bookends, and text is either selected and copied or highlighted the result is a lottery. It may:
a) Work without problems
b) Immediately show problems e.g text copied and pasted into Bookend fields, or highlighted to create a note. Text may (i) be reversed right to left (e.g. nodnoL instead of London, or (ii) you get '' (square with ? inside ) for each letter.
c) text highlighting works ok. for a while, but then starts doing b(ii).
d) Text highlighting seems to be working, you click away from that reference, and then reopen, or quit bookends and reopen and all or part of your highlighted notes have turned to ????????
So far - when I have looked - opening a Calibre-produced pdf always displays correctly in Adobe Acrobat Pro at first. But when problems appear in Bookends, the same issues are displayed when opening the same file in Acrobat Pro. Sometimes the text will no longer be selectable in Acrobat pro. It may offer the option of doing OCR on the file. The file can then be worked with normally in Bookends as well, but it takes ages to save the file when you click away from it in Bookends - not a healthy situation. There is no general 'repair pdf' option in Acrobat Pro (that I'm aware of).
Not being able to use the Calibre ability to format pdf output is a pity if you care about having nicely formatted files to work on.
Alternatives to exporting epubs to pdf are limited. However I have found that onlineconverter has always worked without problems in Bookends for me (doesn't mean that it always will). The formatting can be pretty horrible (or ok) but at least you can then get it into Bookends.
Cheers,
Malcolm