I will always edit the metadata and download a cover if the original one is too small/not the one I want. Also I will run the polish books function to update the cover in the book file, remove unused CSS rules, and compress images.
As far as editing the actual code of the book, when I was using KOReader I could get away with not doing so most of the time. That was because I could choose to ignore font families, margins, padding, etc. within the reader.
Now that I'm trying to use the stock reader (for the Libra Colour note-taking features), I find myself having to remove these things from the code myself, and quite frequently. I really wish the stock reader had some way to
ignore publisher fonts
