XXL, Connecting the two pipes together right after the collectors would not give you a tri-Y and could hurt the scavenging if too close to the collectors. Tri-Y's are used on V8's, because they don't fire evenly with respect to the two header collectors. A cylinder fires on the same side as the previous at least twice, once per bank. Winter eluded to that when he mentioned the four cylinder fired every 180 degrees. A V8 is not as simple as two, four cylinders with two collectors. 5 and 7 fire on the same bank, one after the other. The same with 8 and 4. Six cylinders don't have that problem.
Headers are designed for relatively specific applications. Primary tube diameter is dependent on engine size. Primary tube length is chosen for rpm range. Collector diameter also has an affect on power at certain rpm's. Collector volume (diameter and length) effects the velocity of the gases and that in turn effects the scavenging of the cylinders. If you have a 2 1/2" collector and connect a 2 1/2" pipe to it, all the way back to the mufflers, you have a collector the size of a barn. The gases will exit the primary tubes, loose velocity and come to a stand still. All you have is back pressure. No scavenging and little flow.
If you want to use a single muffler, you should merge them, back away from the collectors in a muffler as winter suggested to you. A "Y" pipe would add restriction unless they go into larger pipe as Sam reported from Flowmasters.
If you're thinking race engines sometimes use a long open collector, without a reducing cone, you are right. They are interest only in how much power they can make at 8000 rpm and they could give a crap about scavenging at lower rpm's.
