I'm not seeing any visual discrepancies between your two files. Both files have a text indent of 1.5em in content0006.xhtml
As i said before, conversion does not preserve CSS, only visual appearance. Conversion also rescales font sizes by default based on the output profile you select. You can disable that in the Look & Feel section of the conversion dialog.
https://manual.calibre-ebook.com/conversion.html#fonts