If you go to the 3.6 version of that doc page and also read the section on finding modules, you'll see that the presence of a "python._pth" file causes -S (skip importing site) to be implied unless the ._pth file includes "import site":

https://docs.python.org/3.6/using/windows.html#finding-modules

You'll then notice that the embeddable distro includes a ._pth file by default (though you don't have to distribute that with your app, just as you may want to omit the exe files). That could certainly be called out more clearly in the section on the embeddable distro, though so far it hasn't come up with anyone who's using it for its proper purpose (that I'm aware of).