> I often find that code alone is not enough to describe why something did or didn't work.
Me too. And I also often find that commit messages alone are not enough to describe why something did or didn't work. Code and commit messages both help.
"Clean history" can obscure things when it leaves out information about the often messy process of creating the software. It's impossible to know ahead of time what information will and will not be useful when attempting to grok a piece of code in the future, so sometimes it makes sense to err on the side of more information, instead of less.