I posted back in 2010 about how to get WiX to correctly deploy a website using harvesting. It was a rather clunky solution that required changes to your development machine (and the same for everyone in your team) as well as any build infrastructure you are running. I have now discovered a much cleaner solution using harvest transforms (tested using WiX 3.7).
As a recap, harvesting pulls files from the project reference compilation into the MSI and puts them into a single output directory. This means that website content and the binaries will be in the root folder of the deployment. This is no good for websites that require binaries to be placed into a bin folder.