This turns out to be a problem with boost installs in general and the source is that cmd.exe doesn’t like paths longer than 256 chars. (see https://stackoverflow.com/questions/60335004/boost-bjam-fails-as-a-cmake-external-project)
The solution for me was to allow cmd.exe to work with longer paths as described at https://docs.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation#enable-long-paths-in-windows-10-version-1607-and-later - but changing the cmdstan install path to somewhere closer to the root of the operating system should also work.