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One way around the TOC limitation is to limit it to high level items but at the top of file that is the destination of a high level link, create a much richer inline html toc that shows the level of detail you want just for that chapter or section.
That way, a click on the official ToC gets brings you automatically to a new html toc so that a second click gets you any where you want inside that destination chapter/file.
FWIW, Epub3 does support fixed page layout (but Sigil does not) but frankly multi-reader support is poor due to differing screen sizes. A pdf is therefore often a better choice instead of a fixed layout epub3. Fixed layout epub3s are often used to target children's picture books.
Sigil targets the more accessible reflowable epub2 and epub3 formats.
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