To preface, I didn’t mean to imply that there are no bugs if you use stock Ebook (!!), and even very simply at that—just that it gets worse the more you try to use the compiler as designed.
Ignore the font changing letter shapes in italic, that’s not on Scrivener. But have a look at the font size.
Setting aside the bad assumptions about character styles having a hard-coded size, the actual problem, as you note, is that all body text is incorrectly set to 0.92rem, and that is caused by…
The section layout styles being added at the very end, i.e. after the user css, is an issue.
Yeah, there is already a thread on that. It shouldn’t be generating anything at all in fact. Those divs are meant to be for your use alone, under the current design. The fact that it inserts this auto-generated stuff, forced to the very end of the CSS file is almost comedic, given that. A tool meant for users to make better books ends up being something forcing users into !important hacks to get anything done.
But even worse, the Section Layout DIV generation is broken too, which can cause formatting from higher levels of the hierarchy to bleed into lower levels as the divs are never generated for lower levels and higher level divs incorrectly wrap around entire child groups. The thread I linked to above shows you how these div classes are supposed to work.
Specifically to the font size problem you noted, it’s not that Emphasis is misguidedly set to 1.0, it’s that the div.chapter-heading section layout is incorrectly wrapped around the entire document, and has itself generated font-size: 0.92rem.
The section layout setting a text-indent is an issue (although this does nothing, as even the base
prule overrides it).
If I understand correctly, that is a noted bug; workaround given in the thread, though I suspect you know how to solve it.