Okay to close off this topic: we have a new branch "optncx" which does not require epub3 epubs to have an NCX, and that uses two epub3 tools menus - one to generate an NCX and Guide from the Nav, and one to now Remove the NCX and Guide.
So no more warnings about creating an NCX on epub3 anymore, but still making it easy to edit your epub3 and before final save generating an NCX and Guide to help with backwards compatibility.
This branch is now undergoing testing. Once we know we have not broken anything we will probably merge this into master for the next release.
For some future version will can worry about making things automatic by default or not and how to let the user control that.
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