I've found generally it's fine for most things but issues come from when the scientific libraries are built with/without certain options. The lack of OpenMP for FFTW is annoying, for example.
$ 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.