OK, that's probably right, but I use a 3-stage method of "building" e-books. First, using Anthemion eCub to assemble all the files in an ePub, then Sigil to modify the structure (and run their Validity Check) to remove the auto-generated TOC and hack the content.opf file, then finally Calibre to "explode" the ePub and make final adjustments before converting to MOBI for Kindle use. I know that files that fail HTML-5 validation also fail Sigil's validation and, when I view it on the Kindle there are subtle layout errors that I believe are created by "open" tags. When I make sure that all <a> tags are explicitly closed I don't get those errors.
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