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Actually, I almost never use the semantics... I just opened a file to see how this is in my books. I have a cover.xhtml which contains, surprisingly enough, my cover. If I look at the semantics, it is specified as cover. The image itself is labeled as 'cover image'. I would add the semantics as a finishing touch.
Myself I use a template epub, which by default contains a coverpage, titlepage and a default stylesheet. The rest I will add later then, but it helps me.
I am not quite sure what you mean with the other part. You can add empty chapters for footnotes or appendices any time. You can change the order of the chapters by just rearrange them in the browser on the left. However, you can also put the footnotes at the end of a chapter. It is just a link to some text in essence. I would not create chapters will you not will use of course.
I don't know if you can add bug reports without a google account. Since I have one, I never checked. Perhaps openid will work?
Feel free to enter feature requests, but Valloric ultimately will decide. And beware, he is not fond of pink bidets... (just search...).
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