You're absolutely correct about the font scaling issue, and the workaround by removing the font-size: lines in the CSS file. You might be interested in a little tool one of the forum members here created for us, which automates the process of parsing and removing those troublesome lines:
https://www.mobileread.com/forums/showthread.php?t=83209
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OK, so maybe this is obvious, but the Kobo reader builds it's TOC by gathering up all of the text in the body of the book that has "h#" tags around it.
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This isn't actually correct. The TOC in an epub is fixed when the epub is created. You can find it in the 'TOC.NCX' file within the epub.
However, most programs (such as calibre) use the 'Heading #' tags to auto-generate this TOC.
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Regardless, the Kobo reader doesn't seem to handle the h1, h2 or h3 tags any differently when it builds the TOC, so there's no point in having H1 tags for section titles and h3 tags for chapter titles. They'll all just look the same in the Kobo reader TOC.
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Most ePub readers CAN differentiate between the heading levels and allow a hierarchical structure like you would expect (like you see in Sigil). Obviously you've noted that the Kobo doesn't have this functionality yet, but it is quite possible that a future firmware upgrade will bring it to us.
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I've also been been inserting Sigil chapter breaks right above the chapter titles. This causes the software to split the current XML file into two, but isn't enough by itself to generate a TOC entry. I have a feeling that the Kobo reader would let you do the "Next Chapter" menu function based on this split though. I'm going to test that tonight.
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It's a good idea to split the HTML/XML files, like you mention, as much as possible. It will help the load times when you flip between those breaks on the Kobo.
However, the Kobo does not use these breaks as indications for chapter breaks.
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I'm hoping that a simple <h3>Chapter XX</h3> will be enough to do the trick.
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Correct. It might also help you to know that you can do this through point&click within Sigil by just highlighting the chapter heading and adding the 'Heading #' style from the toolbar. (it might be worth it to use the 'remove formatting' function first, to remove all those other attributes and tags, as these can sometimes create redundant entries in the TOC).
Happy Tinkering!