Originally Posted by st_albert
But IMHO one still needs to use Sigil to tweak the Indesign-exported epub.
Yes, absolutely. In our workflow (small commercial publisher) we use indesign as a starting point because our pbooks are made with it, but you need some tweaking in Sigil. We also use Calibre for storage and for embedding metadata. We use CS5.5, but a similar workflow worked well in CS4. I'll just throw out some tips based on my experience:
Keep your book as a single long story in Indesign, and split in Sigil. The Book functionality in Indesign with separate docs for each chapter is a huge mess. Make page breaks a separate paragraph containing only a page break with its own para style in Indesign, search & replace in Sigil to make chapter breaks and then split based on those.
We keep an indesign template with appropriate epub styles, and restyle each book based on that. Make sure that headings are properly tagged in indesign (set export tags to Hx in the style). Generate a TOC in Sigil, this is better than embedding a TOC from indesign.
For images we get best results if we add them inline in their own paragraphs, with bylines in a separate paragraph beneath.
Indesign messes up the fonts if you choose to embed them, in Sigil you can remove obfuscation and replace the font files. You miss out on subsetting, but all ligatures and glyphs are guaranteed to be there.
We use Calibre and the plugin Modify Epub for embedding cover+metadata.
Finally, the CSS generated by Indesign contains some insanely stupid design decisions, for instance they hardcode character colour (messes up night mode and other "themes" with dark backgrounds on some devices) and specify font sizes in pt (or px, anyway it's a fixed size). You're better off making your own CSS and replace the stylesheet in Sigil with that. Use relative units like em for text that should differ in size. The only thing we keep from the Indesign CSS is font-face declarations if applicable.
After this process our "Indesign" epubs turn out very nice indeed
If you add semantics->Text at the start of your main text, and generate an HTML TOC which you place at the end of the book, you can also use this epub to generate a mobi with KindlePreview, we've had acceptable results with that.
Don't hesitate to ask if you have questions about this process, the above tips stem from years and years of adventures with Indesign-created epubs.