The epubcheck validation tools does
find more errors than Flight Crew, amongst others the itunes.plist-thingie (I think Sigil strips those out silently, so of course the built-in FlightCrew won't find it), and unusable links in the ncx.
But the point is, that the distributors and resellers - whether we like it or not - use the "official" epubcheck, not flightcrew. So I have made an attempt to make it as easy as drag-and-drop (in windows), which I just published in the ePub forum
It's a windows batch-thing, but similar tools should be easy to implement in OSX and Linux, I think. Feel free to play around with it