pythonPackages.pybind11: apply patch to properly get headers directories

It seems as the `pybind11` build code returns the Python headers
directory (where the `pybind11` headers are stored as well on traditional
setups) rather than returning the dedicated prefix[1].

An exemplary fallout is the broken build of `pyopencl`[2].

[1] https://github.com/pybind/pybind11/issues/1425
[2] https://github.com/NixOS/nixpkgs/pull/56082