It sounds as if InDesign isn't creating a 100% valid ePub (if the untouched ID output is generating validation errors right away). I don't use InDesign so I don't know if there's any configuration options that would affect that sort of thing.
The problem with trying to tweak an ePub 3, is that you need an editor that's capable (which Sigil is not), or you need to unzip the ePub and manually remove the offending DOCTYPE from the ncx. The only problem with the latter solution is that ePubs must be zipped in a very particular manner that is not very intuitive for the casual user (or even possible with some gui versions of popular archiving software).
Out of curiosity; what are your actual plans for distribution? Perhaps you don't even need the ncx (included only for EPUB 2 Reading System forward compatibility purposes). Maybe InDesign has an option to disable the inclusion of the ncx file when saving as epub 3?
Last edited by DiapDealer; 09-20-2013 at 07:47 PM.
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