There are a few issues that I encountered when I tested Scrivener ePub output:
- Chapter suffixes not being properly appended
- Extra spaces appearing after headings/subheadings/sub-sub-headings
In addition, I like to look at the HTML and CSS associated with images to make sure they are not being reduced in size during the ePub compile process. This was an issue I encountered with Word and Pages. So far it hasn't cropped up in Scrivener, but I need to manually confirm this for peace of mind.
Regarding Kindlegen: Scrivener incorporates Kindlegen into the compile process for .mobi files. It's nearly seamless, and generates good output when I test in Kindle Preview and the Kindle app for iPad.