Here's my SWAG on the Peugeot fork: The fork alignment made the fork's resonant frequency more pure since the mechanical shape was more symmetrical. This reduced the mechanical modes at the other various frequencies seen on the misaligned fork. After alignment, you can see more energy at the dominant resonance (31 Hz) and less energy spread around the other higher frequencies. In other words, the fork is more like a tuning fork after alignment and less like a metal blob. There are marvelous tools to do animated 3D FEA simulations that would probably answer this is in more detail if you can find someone who has access to that kind of thing, and the time to pursue it.

Having said all that, it would be interesting to see how the fork rides and feels aligned vs misaligned. The aligned fork should have more tendency to vibrate at 31 Hz since the peak of the response is higher.