Very good practical idea to fill up the trunk volume. Ideal fill would be foam pillows from furniture, sleeping bad pads, folded beach towells, etc.

A quick test of whether metal to metal contact of the exhaust pipes is influencing the drone noise would be to buy some inexpensive high temperature rated, but flexible Silicone cookware pans, cut it up into small spacer pads, insert these pads into tight areas, and hold in place with those stainless steel cable ties.

A quick cheap test to see if a bit longer muffler would reduce the drone would be to insert a socket into the end of the exhaust pipe and temporarily hold it in place with a vice grip. This creates some additional back pressure that can be adjusted by changing socket size.