I use the calibre editor. The things I nuke outright are embedded body font, body margins, line height, atypical body font size - those just go via the mass Find & Replace. Spaces between paragraphs (if there are any) and text indents other than 1em need editing, not just nuking. The next thing on the menu are blockquotes, poems and such; sometimes their margins need fixing. I don't much care what chapter headings look like, unless they have a huge margin/padding as large as half the page. Sometimes the TOC needs fixing too. Widows and orphans I set to 1 for my Kobos, to avoid large gaps at the bottom of the page, and I disable hyphenation.
All in all, most books take only a minute or two.
I knew nothing about css/html either when I started to fix my books; but I was just too annoyed by various things to let it rest. I couldn't enjoy reading my books unless I fixed the formatting.
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