Yes, you can store both in the trunk with careful folding/packing. Exhaust may actually be louder depending on if the side windows are cracked open or not. The cost is expensive, especially after custom fitting. I don't recall what ERA charges for this. My car also has the fitted tonneau cover. Can't see how I could drive with it, though. My seat is all the way back, so where do you store the driver side when in the seat? Also, it will flap/beat on the top of the doors at speed - not good for paint.
