When I want to create a mobi file that I can upload to Amazon, I prefer to use eCub or Jutoh, because you can use Amazon's kindlegen tool with them. (selfpublishingadventure.com)
The best way to handle these differences is with a special construction in the CSS file which will be used by KindleGen to make the needed changes in the file. (wiki.mobileread.com)
Basically, it is more efficient now, for me at least, to send the file I create with KindleGen to different devices via the Send to Kindle app. (goodereader.com)