The crossover is running between the header pipes on later XL's and is hidden behind the lower pipes (earlier XL's have the crossover right below the air cleaner in plain site!). If you replace your mufflers, you'll see the pipe!
The crossover pipe also helps with noise abatement. HD has to meet certain noise emission requirements for some localities that have sound level restrictions. Since the cylinders fire at different times, if you send the exhaust gas and noise through two mufflers instead of one, you have cut down the "loud" factor as each cylinder is "double muffled."
It also helps with engine scavenging of the cylinders, in that when one cylinder is firing, the other is charging and the exhaust valve is usually still open during the "filling" process to allow the air to "flow through" providing a better charge in the cylinder. When the other cylinder fires, the force of the exhaust helps to "shove" the fresh gas back into the other cylinder through the slightly open exhaust valve and ensures a more efficient charge and use of fuel.
This process is actually helped along by not only gas pressure in the exhaust, but also by sound waves in the exhaust. This characteristic is actually more prevalent in 2 stroke engines than in 4 stroke, but depending upon what you are looking for (low end torque or more high end horsepower), it can come in to play when selecting replacement headers or exhaust.
I went with the HD SEII slip-ons and the SE air cleaner. After re-jetting, according to the book I should have an additional 9 HP over stock. I can believe it. My 2006 XL1200C sure runs a lot smoother and the original slight backfiring is gone. I do intend to put it on the dyno when I take it in for the 5000 mile service next month, if anything just to satisfy my curiousity.
There are a lot of good exhaust systems out there, and it really comes down to effective research AFTER you have sat down and seriously decided what you expect when you are finished: A touring bike, or a 1/4 mile dragster!
I ride with a group of HD owners from my office, and they all have bigger cruising bikes. On the road or in town, I can out accelerate any of them with my XL1200C. And I do like the performance and handling!
Good luck!