It is an error to use a section registered as allowDefinition='MachineToApplication' beyond application level. This error can be caused by a virtual directory not being configured as an application in IIS.
I went back to the comments from the blog post and found this one, where someone else was having the same issue and they solved the issue by deleting the obj\
That also did not work for me, so I followed a link to the use of Web Deployment Projects with ASP.NET MVC and noticed that they were using the following PhysicalPath setting.
I changed my setting to this value, $(ProjectDir)\..\Web created this directory and now things are working properly again.