What is that extended nacelle feature on the Honda HA-420 HondaJet?
They aren't covers; they are fairings to integrate the flow going past the lower part of the cowl with the exhaust stream coming out the tailpipe above and the pylon below.  It's because the cowl extends below the engine some distance to house various parts like accessories, plumbing, ducting etc.  You have to create a nice transition for the airflow or you would have a lot of unnecessary drag.  

You could say that the fairing is filling in all the 3 dimensional space that the free stream and the exhaust plume can't fill in because the change in direction is too extreme, and would result in flow separation, causing turbulence/drag.