The default setting for "Full Path of Source Code File in Diagnostics" seems to be set to enabled. In Visual Studio, if you open the project's properties and navigate to Configuration Properties -> C/C++ -> Advanced, you will find the "Use Full Paths" property, which is enabled. You may also recognize that it is printed in a non-bold font, indicating a default value. Set it to "no" and it turns bold.

Saving the project will add a line to the .vcxproj file:

[...]
<ClCompile>
    [...]
    <UseFullPaths>false</UseFullPaths>
</ClCompile>
[...]

Obviously, CMake needs to add this line to explicitly disable the compile flag. However, from a search of the repository, we learn that there is currently no implementation to achieve this. The FC flag is mapped to nothing or to true:

[...]
{ "UseFullPaths", "FC", "", "true", 0 },
[...]

CMake should provide a way to disable /FC