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The best way to get a well-formatted ebook is to edit it manually with Calibre editor or Sigil. All the bulk operations with Quality Check, Modify Epub, Polish and so on only go so far; they don't really fix broken formatting.
That said, few folks can be bothered to edit all their books manually. Most just manage with what they have.
As to whether your workflow is a good one, it's good if it does what you want. Everyone has different goals and does things in a different way. Personally I don't do all this bulk checking and fixing - I don't need most of that, I fix the formatting manually and fill the metadata in manually too. It's just faster for me this way. I do use Modify Epub for a couple of bulk changes, but not for fixing bad formatting.
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