Well, I can only offer opinion.
In my opinion, positioning the APPS on the pedal is "the way it should be" for drive-by-wire throttle arrangements. This means one less hole in the firewall to pass a cable or wires, one less underhood component, and the APPS remains relatively protected from the elements in a convenient little package right under your foot.
Not sure how much they cost relative to mounting underhood, but I suspect it's cheaper (otherwise, why would they do it?).
Ryan