I couldn't care less if the code is clean or nasty or in between. I don't care about epub errors either. In fact I never check for them. The only thing I care about is for the book to look like I want it to look on my ereader. So I fix only those few things that matter to me, like line-height, indents and spaces between paragraphs. The rest I leave as it is. A working TOC is nice to have, but not that important. Generally I won't bother with it.
Still, I do fix these things in the editor, not by conversion. And I delete excerpts, ads, praises, recommendations and other fillers, because I can't stand them. I've never understood the point of excerpts. If I like the author, I'll buy their other works anyway (at least some of them), and if I don't, no amount of excerpts will make me to do so.
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