There seems to be many things Adobe can do to improve the out-of-the-box ePub creation mechanism to reduce (or potentially eliminate) the effort publishers must go through in order to make their ePub files compliant with the latest ePub validation tools, as well as eBook distribution centers. This is a working list of problems encountered from my inDesign CS5.5-produced ePub:
Tools used to validate ePub files were epubcheck-1.1, epubcheck-1.2, epubcheck-3.0b3, FlightCrew, and Lulu's file upload for eBook distribution service
Tools used to produce the ePub file and edit the file contents included inDesign CS5.5, Dreamweaver, and Microsoft Notepad
As I anticipated, when I regenerated the ePub file from inDesign CS5.5 without including a cover image, I am no longer getting the "this resource is present in the OPF <manifest>, but it's not reachable (it's unused)" message. I hypothesize that the error message came to be because the cover image was not embedded in any .html document as part of the eBook, though it was defined in the content.opf.
My epub file is now error free.
I will leave this in "unanswered" state, since I would love for someone from Adobe to look at this and consider how some of these alledgedly inDesign-caused errors can be fixed.
This is a user forum, not a channel to tech support, so it's pretty unlikley that "for someone from Adobe to look at this and consider how some of these alledgedly inDesign-caused errors can be fixed" is going to happen, particularly since you posted in the Feature Requests forum rather than genereal discussions. You won't get someone from Adobe there, either, but you will probably find other users with epub experience who can offer advice.
Maybe someone from Adobe will get drunk one night and accidentally arrive here when they really intend to shop online at Toys R Us? You know, kind of like a room full of monkeys at typewriters accidentally writing War and Peace? I could happen. Don't be so fatalistic.
CD@TriscellerPub, I found a resolution to one of your problems above, I believe. It is the message from Sigil that states for the cover image the following: "this resource is present in the OPF <manifest>, but it's not reachable (it's unused)"
I could not find a solution anywhere but finally figured it out through a lot of trial and error.. It was Lynda's training course, (thank you Anne-Marie Concepcion), that at least gave me the skills to poke around and figure this out. It appears that a <guide> variable needs to be set to fix this in the content.opf file. Since I added the <guides> to the content.opf file, following Anne-Marie's directions with my last book, before running Sigil's checker, I had never seen this message before. So for folks out there that have never seen this error message that might be the reason why.
The cover image showed up fine in Caliber but not in Adobe Digital Editions.
The Sigil error message is the following, "This resource is present in the OPF <manifest>, but it's not reachable (it's unused)" which is an obtuse message to say the least. It says it is "not reachable" and it is "unused." The "unused" part seems to be the key because it was very "reachable." (it was there, referenced properly and named properly) This error message was on the cover image that I was telling InDesign 5.5 to add from a file when I generating the EPUB.
When building my EPUB, InDesign 5.5 added the following lines in the content.opf file:
<meta name='cover' content="cover"/>
InDesign adds no <guide> statements to the content.opf file. I added the following to get rid of the error message:
<reference type="cover" title="Dust Cover" href="images/cover.jpg"
Warning, there may be typo's above.
Hope this helps.