@Isamilis: Start with enabling "disable font size resizing" option in Calibre's Convert window (under Look& Feel > Fonts). Convert the same source file with Calibre, kindlegen and Epubor , then compare the results. With font resizing disabled Calibre's output mobi/azw3 should be almost the same as what you get with Kindlegen.
By default KindleGen creates "dual mobi" AND includes source file (epub) also , that is why you get doubled filesize at the end. There is "-dont_append_source" command line parameter/switch for KindleGen that instructs it to not includes the source files.
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