I can help you with a couple of things, but, you are correct, some of the ebook handling doesn't work well.
Regarding the font issue...Bold and Italic don't drop out if you use font attribution and not actual bold and italic fonts. As a book publisher I discovered this when we were looking at why some of the fonts dropped their attribution and others didn't. We alway substitute an actual font when printing. for ebooks, however, they will drop out. I think that has something to do with the CSS only allowing 1 font per style. this probably wouldn't be a quarkxpress issue. certain fonts are blended fonts, meaning they don't have separate fonts for bold and italic. I was always taught never to use attribution. however, for ebooks, it works.
Regarding Component Insertion...I'm not understanding what you mean exactly. But, let me tell you how I prep my articles. First, an ebook breaks based on the articles you create. So, what I do is use Linkster to break where I want the articles to break. for example, I want the title page as a separate unit, I want a chapter as a separate unit...whatever I want as a separate item I split the page flow accordingly using Linkster. When I want to make sure an image or dingbat stays with the article, I embed it. this seems to work well.
Regarding redoing work when the print document changes...Yes, this could be problematic.As far as I can see, reflow text does not update when you update your document. This does mean you have to insert the change in the reflow text or delete the reflow text and do again. This isn't a problem unless you've taken the time to rename your articles for the TOC. Removing the reflow also removes those names. I reported this as a bug to Quark and hopefully, when 9.2 comes out, they will fix it.
About CSS use and your books...We are having a problem with fonts (of course) because of how the licensing is written for the font people. I'm trying to find a workaround so I can use @-font-face in my CSS without breaking licensing agreements.
If you'd like to chat sometime, let me know.