Only thing I can think of is it is a much easier way to route the pipe. The way you did it required wrestling with the drive line, gas tank centers of x-members, etc. putting it down the space between the frame and the guts of the car in the middle allow it to tuck neatly in an otherwise unused space. Also lends itself to dual exhausts.
I see a lot of rods with dual megaphones directly in the middle of the back of the car. Barris' Ala Kart had 4 pipes directly in the middle. VW bugs have a megaphone directly in the middle.
May be a very slight safety advantage too since air currents directly behind a car are strange and there is often a negative pressure there which will draw combustion gasses back to the car. A side exhaust has cleaner air flow to blow the ehauxt past the car as it moves. Wouldn't worry myself too much about it!