I would guess that the reason the automatic shifter is in the center console is because if the same model offers a manual that is where the shifter has to go and it would be expensive to have a different center console arrangement on the same model betweeen the two transmission options.
I agree that on models that don't offer a manual tranny option the reason for putting the automatic shifter in the center console is the same reason that the car has a tachometer in the dashboard (recent discussion on this should be easy to find). That is because buyers (targetted by that model) think that is "cooler" than putting the shifter somewhere else.