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No, using headers as chapter titles is normal. If you generate the TOC in Sigil, all the correct links are there. Depending on the conversion to Kindle method, it will work. I think the Kindlegen does not take the ncx (standard TOC of the ePUB) into account, but Calibre does. Then again, it could also be vice versa.
I don't know how Word saves bookmarks and hyperlinks as HTML by default. In my macro I have that covered as standard HTML. It saves a whole lot of code which you will not use anyway. It might be the reason.
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