Yes, that's of course a potential issue with any distribution. The good news is that's relatively easy to tweak their recipe to build your own version.

  $ conda install conda-build # prerequisite...

  $ https://github.com/conda-forge/fftw-feedstock && cd fftw-feedstock
  $ emacs recipe/build.sh # Add --enable-openmp

  $ conda build recipe
  $ anaconda upload -u mychannel ${CONDA_PREFIX}/conda-bld/*-64/fftw-*.tar.bz2

Now you can install your custom-built version of fftw and easily share it with your friends by telling them the name of your channel on anaconda.org.