What is happening is that when a project is built in Visual Studio some targets that are external of the whole process that were installed as part of Visual Studio are used as part of the process. Obviously, when we run MSBuild via cmdline, we are not setting the parameter “VisualStudioVersion”, because this is pretty much a “headless” build. So the sqlproj file handles this by setting the parameter to 11.0, which is pretty horrible. Given that projects are created in Visual Studio, I would’ve felt that the version a project was created in would be baked in as the default, as opposed to just some random version number. At the very least, a warning that a default version number has been set would come in useful, especially as this is 2016 now and the sqlproj files default to 2010 targets.
Fortunately, Richie has the answer to this issue.