Is the MSBuild in the Microsoft Build Tools 2015 capable of building projects that use MS Fakes?
https://www.microsoft.com/en-us/download/details.aspx?id=48159
As far as I know, in order to build projects that uses MS Fakes, you need visual studio enterprise edition (look at testing tools comparasion).
VS 2015 Enterprise is setting up several files into MSBuild tools folder, which includes msbuild targets, and also some *.dll, which contain MSBuild tasks eventually to create fakes binaries.
Summing all up: MSBuild in the Microsoft Build Tools 2015 is capable to build projects that use MS Fakes if you have VS 2015 Enterprise installed.