I always thought, calibres conversion feature is aimed at readers not authors. It is there to convert from one existing format to another. Automatically, regardless of the quality of the source.
If you want to make a quality eBook, then use the calibre editor. Or Sigil. To produce a kindle file, there is kindlegen from amazon themselves. Or even convert with calibre. You won't edit the file anymore, since you would do that in the source file.
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