I remember having read somewhere that the Kindlegen tool packs (at least parts of) the source epubs into the ebooks. It was mentioned in the context of debloating the books. AFAIR If you used an epub as source it is added as a whole to the contents of the Kindle ebook. If you pointed to a folder of a decompressed epub, only the parts needed for structure are added, so that you don't double the content. Both would explain the preservation of internal names.
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