I have a 289 Cobra replica with a 3.9 Rover. The exhaust has morphed over the years from two unconnected pipes - nice sound but kinda lumpy, to a system with a balance pipe - better smoother running, to an X pipe - much better, crisper throttle response and improved torque.
The joining of the two separate pipes aids exhaust gas extraction from the cylinder (scavenging). Ideally pipes from opposing sides of the engine should be collected together in one side of the exhaust, which pipes depends on the firing order of the engine.
The Cobra has long tube four into one headers and a 2" system with two cherry bomb type 'silencers', there is no reduction in internal diameter all thru.
The best results are obtained by fitting the balance pipe as close to the headers as possible. A balance pipe will give a more period correct sound whilst an X pipe gives a TVR type howl.
My P6 has two separate side exit pipes with cherry bombs and a balance pipe behind the sump. It has only just had a 5 speed transplant and I have not had chance to drive it on the street yet, it did sound good with the auto box but taking 4 kg off a std flywheel and fitting the manual box has totally changed the sound to a sharper barkier tone from more of a woofle.