I'd just look at an x-pipe and a decent resonator/muffler. I wouldn't mind having more tone at 50%+ throttle and enjoy the somewhat mellow exhaust growl it has under acceleration. But I agree that the 3.9 V8 doesn't have enough mechanically to make that low rumbly tone when people think muscle car.
Tone is all a factor of exhaust pulse pressure, exhaust volume (cfm), and how you modify them down the pipe. This is why a civic will never sound like a 3.9L, and why a 3.9L will never sound like a 454. Can you make them sound similar at some point? Sure, if you try hard enough and accept degraded tuning, anything is possible.
I would think of the cylinder/piston like speaker cones. Say you have a 8", 10", and 12" speaker. If you take your finger and flick each cone, you get a different sound for each one. The act of flicking the cone would be like the exhaust valve opening in the head. That's the initial event that starts the whole thing.
Now, you can modify those tones by use of boxes, baffling, porting, bandpass, etc etc. And sure, you can find a point at which they over-lap some, but for the most part they will sound different. This is because each one produces a different amount of air displacement at different pressure levels.
So, that's my explanation.