You misunderstand what is shown in that video. First, the
microphone is not to blame—it accurately converts pressure to voltage (with the correct sign!) in the frequency range of interest. Second, only the
acoustic transfer function (i.e. the sound pressure) is relevant to this discussion.
The cone motion being out of phase with the pressure above the system resonance frequency seems curious at first glance, but indeed follows directly from the physics involved,
as explained in this thread. Sound pressure in free space is proportional to the diaphragm acceleration, which is 180° out of phase with the displacement. Do note as well that the displacement is
not in phase with the input voltage except near DC.