I remove page margins, paragraph margins in main text, give justification and indentation of 1.5em. I usually spend some minutes, no more, but sometimes I commit myself more, if the book is complex or I need to learn something (about calibre or css).
In rare occasion I remove and Create again the TOC because it is so poor that I need to change it - for example a dictionary of metric and rhetoric had no TOC for alphabetical order - but generally I don't do it.
May also be that I buy a book from Kobo and I am satisfied enough with its formatting so I simply read it. And of course it also depends on how much time I have available.
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