The article doesn't imply it's a mystery, only that simple one-liner explanations are insufficient. The headline is reasonably clickbait-y.
The momentum theory of lift is simple, intuitive, but unfortunately incomplete (just as the differential pressure explanation). It's covered in the article.
> But taken by itself, the principle of action and reaction also fails to explain the lower pressure atop the wing, which exists in that region irrespective of whether the airfoil is cambered. It is only when an airplane lands and comes to a halt that the region of lower pressure atop the wing disappears, returns to ambient pressure, and becomes the same at both top and bottom. But as long as a plane is flying, that region of lower pressure is an inescapable element of aerodynamic lift, and it must be explained.
Also I want to address this:
> At fractional mach numbers, pressure above and below the wings is essentially equal.
Surely you mean density? Air pressure is certainly not the same above and below, as differential pressure integrated over the surface is equal to the lift force generated by the wing. So no, while the Newton's explanation is a great explanation for a second grade classroom, it is not complete.