I have both File Roller and Engrampa Archive Manager installed, as I
have both the Unity and Mate desktops installed.

File Roller dos not open ePubs, Engrampa does.

Maybe you should talk to the people at Mate.

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https://bugs.launchpad.net/bugs/887331

Title:
  file-roller cannot open filetypes with derived mimetypes (e.g. epub
  and ods files)

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