Let's see if I can get this across better. You seem to have a good grasp on basic wave theory - this helps. Bear with me, I am not a great teacher.
"Is the effect on torque in relationship to the collector a factor of flow or exhaust pulse?"
It is a combination of cam events, velocity, pulse tuning, and flow - in combination with temp, and a whole lot of lesser factors.
Pipe inside diameter determines area and thus velocity - or where the peaks occur.
Pipe length alters when the waves are reflected back to the cylinder(s) and can be used to rock the peak torque and power points by several hundred rpm or to fill in dips in the curves.
Exhaust pulses reflect both ways in the exhaust flow, and act as both positive and negative waves. They occur in the primary and secondary (collector) pipes and travel between the cylinder and the silencers. So there are lots of waves occuring in the exhaust that change with rpm and throttle opening. Making even more complex waves.
Pulse tuning and scavanging are VERY important to how an engine performs - MUCH more than double amplitude due to the dynamic nature of the engine. But it is a trade off if you need to perform over a wide rpm range. You take what you can get - without robbing too much from other rpm zones by causing negative wave tuning.
This is a bit overly simplified, so bear with me if you already know this.
When the cam opens the exhaust valve, the high cylinder pressure gets a chance to blow out into the exhaust. Think of it as an elongated egg of pressure that travels to the end of the primary header pipe. When it meets a bigger volume opening in the collector, a suction wave forms that acts like a sound wave. This suction wave travels back to the exhaust valve and (if it is still open) into the cylinder. It helps to pull fresh air and fuel into the cylinder and out to the exhaust. This is called scavenging and it helps power - a lot. Think of this like a scavanger hunt where everyone is trying to collect the same things - fuel and air.
It happens again at the end of the collector.
At some rpm points, the suction wave will travel back up the header and meet a closed or closing valve. At these parts in the rpm band, the suction wave can do nothing, or even hurt flow if it reaches the valve at the wrong time. (This is where a cross-over between pipes can help at lower rpm)
In reality, the suction wave reflects back and forth in the header tubing several times, and causes both positive and negative reflection waves. The temperatures and pressures in the header alter the speed at which these waves travel - the tubing length and diameter plays a part in when they occur - based on cam timing and engine flow.
Cam timing (when and how long the valves are open, and how much the intake timing overlaps the exhaust timing) is the heart of the engine.
A four-stroke engine rotates twice (306 degrees times 2) before all cylinders get a chance to fire. That means that the exhaust pulses in a three-cylinder engine are 240 degrees apart. If the exhaust is designed correctly, a group of three cylinders are far enough apart, the suction from one cylinder can help scavange the other two cylinders. It happens in all milti-cylinder engines, but groups of three (240 degrees apart) work together best (3,6,9,12-cylinder engines).
All of this also occurs in the intake, but to a lesser degree.
Have I made things worse?