If you dig far enough in the car, you'll see how extensive the measures are to reduce noise, vibration, and harshness. From the way things are mounted in the engine bay, attenuating foam in key areas of the engine, to the extensive double layer gaskets in the doors, etc. The engine covers are just another layer of that effort. All together, they make for one of the smoothest and quietest riding SUVs on the market. Even with AT tires.
I like to wrench. Yet I like the buttery smoothness of my Lexus. The covers easy enough to remove when I need to service the car. So I leave them on.