You configure with -DCMAKE_CXX_FLAGS='-march=native -ftlo' like any other cmake build. Or you `-G'Unix Makefiles' and export CFLAGS/CXXFLAGS before you build it if you really want to use make.
You should still be OK although I agree that CMake is really annoying to approach if you don't know the projects idioms particularly well e.g. there is a recurring bug in one of our builds where OMP initialization causes a deadlock, which can thus be disabled by not using openmp at cmake-time: finding how to do this when I went to disable it permanently took a good 20 minutes of guesswork because it's CMake magic versus make bullshit