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Even though the conversion process is always the same Input -> OEB -> output, different input will produce different output. Converting to HTMLZ (or any other format) then converting that instead of the EPUB will introduce differences in the final output.
Think about this converting a VHS to an MP4 file vs a DVD to an MP4. No matter what you are going to get similar output (the save video content) but there will be a difference in how the final output from each input looks due to differences in what the inputs support and how they are structured. Even if you were to take an MP3 and a WMA and convert to AAC you will still have a very different output file even though they sound alike.
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