I have a small after market system with a ported 8" and used to have ported 10". I've run nothing close to two JL 12", but I have not noticed the cover vibrating with the system on or off. The cover is a thick cloth that stretches fairly tight. However, with enough air movement I am sure it could probably vibrate and so would any normal light weight non porous cargo cover. You could probably a) weight it down with modifications on the bottom and forgo the easy retraction, 2) build something out of grill cloth yourself and use the cargo cover notches to attach it over the area. Or maybe you get lucky and it works out as is.
The attachment points already have some felt but you can add more if there is concern of those making noise.