That's a very good point, although the kit I have (SPAL and Autoloc universal power window kits combined) basically slips over the manual crank mechanism - in the event of a motor failure, they even provide a T-handle to engage the manual crank to raise/lower the window manually. So essentially, the hand cranks would still work without worry of breaking anything off. There are some little black caps that cover the holes in the door panels, but they're pretty noticeable, actually.
Those white spots on my doors are the nylon gear adapters for the motors slipped over the manual crank shaft (I hadn't put the black caps on yet). Those 'bumps' on the front face of the center console's armrest are the switches.
I also just have a 4-pack pod of switches on my center console (so I didn't have to run a second set of switches over to the driver side door, or something like that). My ebay center console was damaged on the area of the armrest box above the ashtray, so I just trimmed things up and located the switches there.