I hate to be the bearer of bad news, but I just found a bug in the new release. The links to the page-template file are not being removed. I'm using the almost the same options as the screen sent you before except the cover options are not selected.
Code:
Modify ePubs
Logfile for book ID 152 (Star Trek: Typhon Pact: Plagues of Night / David R. George III)
152
Modifying: C:\Users\Jon\AppData\Local\Temp\calibre_0.8.54_tmp_pxljof\thvdmq_modify_epub\152.epub
Looking for files to remove: [u'iTunesMetadata.plist', u'iTunesArtwork']
Looking for files to remove: [u'META-INF/calibre_bookmarks.txt']
Looking for files to remove: [u'.DS_Store', u'thumbs.db']
Looking for unused images
Removing unused image: ops/images/9781451649574.jpg
Manifest item removed: images/9781451649574.jpg (my--cover--image)
Looking for Adobe xpgt files to remove
Found xpgt file to to remove: ops/styles/page-template.xpgt
Manifest item removed: styles/page-template.xpgt (pt)
Looking for Adobe xpgt xhtml links to remove
Looking for Adobe DRM meta tags to remove
ePub updated in 0.96 seconds