[Putting on mathematician hat.] This is because matrix multiplication correctly defines composition of linear operators. It's a "natural" definition independent of choice of basis. I don't even know what notation would be used for element-wise operations, short of "Let c_{i,j} = a_{i,j}b_{i,j}."

Carrying over this to code is of course an advantage of this PEP, but function call syntax isn't avoided in papers due to its readability.