Valid HTML/ePub does not equal "will always convert perfectly to a mobi." Read the Amazon Kindle Publishing Guidelines
to learn how best to prepare HTML/ePubs for conversion with Kindlegen/Kindle Previewer.
There are perfectly valid things you can do with an ePub (and that calibre will make allowances for), that just won't work with Amazon's official tools. There's quite a learning curve—which is what tends to make calibre more attractive to many people.