Can you use the Preferences > Conversion > Common Options > Look & feel > Styling and check the boxes at the bottom for Margins and Padding? I have all of them checked. For my kindle I download the books in EPUB format, then convert them to AZW3. If it's a book from amazon, on the Manage Your Content and Devices page I've set the Default Device to Kindle Cloud so that it doesn't send the book to my kindle, then on the page that lists the books I click on the 3 dots button and select Download & transfer via USB. Then add that to calibre and convert it to EPUB, then delete calibre's AZW3 and convert the EPUB to AZW3; at that point it's ready for calibre to send it to my kindle. The conversion removes all that styling stuff whose boxes I've checked.
