The size of the exhaust does not guarantee flow. With the 2 into 1 exhaust there are several things to consider. Skinny pipes cause stronger pulses and are easier to get resonating, unequal length header pipes can cause interruption at the collector. If you are using fat pipes, it is difficult to have a tail pipe which is twice the cross-sectional area of one of the header pipes. If you make a 2 into 1 pipe with a tail pipe the same size a header pipe, you can easily lose 2000 RPM of the top of the usable rev range, when compared with separate pipes.. Another thing is the timing of the opening of the exhaust valve. A 2 into 1 pipe usually requires earlier opening to get a stronger pulse in the pipe and get the tail pipe working properly. For al intents and purposes, the flow of gas is continuous, but the pipe needs to resonate strongly without any bumps in the gas flow.
With racing Triumphs, the 1953 race kit had skinny pipes when all road bikes had fat ones up until the first Bonneville came out in 1959. The skinny pipes were better.
My 850 motor has threaded stubs and slip joints with springs at the head to hold the exhausts on. There are no steps anywhere because the ID of the stubs matches the outlet of the exhaust port. What happens in the pipe is sonic, any mismatch in ID causes an obstruction to flow.
With jetting, the needle and needle jet are critical, the main jet is less important but should be slightly rich. On most race circuits, you don't use the main jet long enough to be of major importance.