Is the later just a synonym of the former, or are they two different implementations of FFT? Which one is better?
Looking at the github respositories for each, scipy is not just importing numpy's version and renaming it (although it does borrow some functionality). You'll have to dig into the code if you want to discern the difference in implementations since the documentation doesn't make a direct comparison.
https://github.com/numpy/numpy/tree/master/numpy/fft
https://github.com/scipy/scipy/tree/master/scipy/fftpack