What you are see is not so much how much is flow but more, how it is flowing. Typically transfer ports are designed to direct incoming charge across the top of the piston and towards the back cylinder wall. Boost ports are usually directly steeply upward.

Remember, loop scavenged engines were originally designed with 2 transfer ports that directed fuel across the top of the piston that, among other things, helped cool the piston. (These ports also direct the new fuel/air charge away from the exhaust port eliminating the need for a baffle on top of the piston and reducing "short circuiting" ). The boost port was added later to help direct the main charge towards the top of the cylinder.

What you are likely seeing is the effect of how the gasses are directed out of the ports. Given that the ports are not all the same, it shouldn't be a surprise that there are also different temperatures and soot patterns.

Bill