The extra few watts of power the factory amp provides might make the speakers sound a little better at moderate volume, but that amp is not very clean or powerful, which is why most people bypass it. I ran into the same thing, where using just HU power isn't quite enough to get my door speakers moving at low volumes. An upgrade to a better amp for the door speakers is a good next step.
As for the factory speaker "case," I'm not sure why Ford enclosed the speakers - maybe for weather protection or something. In any case, aftermarket speakers don't need all that plastic.
