The TOC-first-level-only issue is worse than I thought it would be. Some books have only the NCX TOC (reasonably enough); there's no HTML TOC at the front of the book that you could use as an alternate. Navigating top level 'sections' is pretty worthless. And it isn't just computer books we're talking about, 'Pride and Prejudice' has a 2 level TOC.
I was hoping to use Nook for my O'Reilly computer book collection because of somewhat better formatting and ability to more easily navigate hyperlinks (than my Kindle). But at least the ePub version of the book I'm looking at has no HTML TOC. So effectively there is no TOC, since Nook won't show the entire NCX TOC. There are 80 or more pages between each top level TOC item. In this case there's a workaround: since they are DRM free, I can write a script to flatten the TOC. But they need to fix this.
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