You can't not include native libraries, at least if you want your benchmark to be realistic. Almost every Python library where performance matters is written (at least partially) in a compiled language.
Yes, but many people like the sound of "X-times faster than Python" while conveniently forgetting that the same thing can be (and usually is) done in Python + numpy & co. even faster.
I have come to appreciate "slowness" of Python. It trades speed for legibility, which is a great compromise once you have really fast native libraries one import away. Best of both worlds.
C++ with well-optimized libraries should always outperform Python with well-optimized libraries, right? They should be ~identical in the highly optimized inner loops, but Python has more overhead. But naive hand-written C++ could easily perform worse than something like Numpy.
(I've only tested this once, and my naive hand-written C++ was still twice as fast as Numpy, but that was only on one specific task.)
