This bug has finally improved in Ubuntu 17.04.  There are only 2 errors
left:

# update-mime-database /usr/share/mime
Unknown media type in type 'all/all'
Unknown media type in type 'all/allfiles'

However it is not clear to me which file is responsible for this:

# grep -r all/allfiles /usr/share/mime
/usr/share/mime/all/allfiles.xml:<mime-type 
xmlns="http://www.freedesktop.org/standards/shared-mime-info"; 
type="all/allfiles">
/usr/share/mime/packages/kde.xml:  <mime-type type="all/allfiles">
/usr/share/mime/types:all/allfiles


** Tags removed: i386
** Tags added: xenial zesty

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https://bugs.launchpad.net/bugs/289592

Title:
  Unknown media types in /usr/share/mime/packages/kde.xml

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