The reason why the exhaust needs to exit in front of the rear seat is simply because the fuel tank is in the way as it takes up all the space between the frame rails under the rear seat base.It appears to me (providing there's room) a better location for the muffler would be along side the swing arm under the rear cover. Aerodynamically that's one more part not hanging out in the slipstream. A less obvious advantage is that by dumping the exhaust into the low pressure area behind the Kamm cutoff it may even raise the pressure slightly, contributing to aerodynamic efficiency. Of course this would need to be verified in a wind tunnel.
The good news is that the exhaust should be tucked up, out of the slipstream, between the frame rails and should not hang down below the vehicle.