You would be correct in your thinking for a POWER ADDER like a turbo or supercharger, it does exactly what you described, because its forcing more air into the engine but not a pipe, it doesnt add any FORCED airflow into the intake of the engine. The intake is done soley thru the carb and via the piston/case/transfer ports. The added airflow is simply from the increased scavenging effect and the loss of the 3 into 1 pipe, creates alot of back pressure and impeded flow. The air intake remains the same, the engine can only flow "x" amount of air thru the port openings,carb opening etc., the only way to change that "x" amount of airflow is to port the cylinders, bigger carbs or a power adder which in turns adds pressure to the air intake! While a expansion chamber will add power from the reversion pulse, but its still only allowing you to burn left over fuel charge that has escaped into the pipe, and this rides solely on the effect of the rear cone of the pipe. It can not create more air intake pressure in the cylinder.This is the sole reason why a expansion chamber was a major break thru in 2 stroke engine design.
This is caused by the exh giving a double pulse action back to the engine,there is a negitive pulse and a positive pulse. The positive pulse reaches the rear diffuser cone and stinger,and part of the wave will be reflected back as a negitive wave and help to evacuate the cylinder of any old charge, by going out thru the cone and stinger, it creates a vacum signal, but the other part of the wave is reflected back at a certain speed depending upon cone angles, that helps to recover some of the lost fuel/air charge that wasnt completely burned before the piston closes the exh port, this is what increases the power and reduces fuel consumption. I am sure you know all this already.
As far as your jetting theory, If your on the pilot jet at 8000rpm....., you have issues, the timing issue that you think is causing all this is on the needles/main jet transistion period. The need for more fuel is the increased airflow thru the engine via the pipe. While yes a viper box has more timing in the first part then a srx does, this helps the engine make more power at a quicker rate, so yes......... a viper box will make more power with triple pipes on a viper then a srx box on a viper will rapidly accellarating the engine! I do know and agree with you that the box has alot of timing in the upper mid range of the box, it was obviously needed for the engine to perform with the single pipe, but it is not the SOLE reason for running large jets all the way from pilot to main, the pipe has more influence then the timing does. The added timing simply puts more heat into the piston, retarded timing puts more heat out in the pipe of the sled, you have to have both, heat in the piston and pipe to come up with a good result.
Your trying to compare a srx exh system to a aftermarket system, and your comparing apples to peas. No one can or will commit the time that yamaha has put into the factory srx exh system. Talking to any aftermarket pipe builder will yield you the same results that you can not out do the factory triple pipe system on the srx on a stock engine, and unless your into a large over bore 78+mm,stroking the engine, or massive race tuning via wild porting,ultra high compression, case milling etc, then will a aftermarket set of pipes be the answer, but by doing that to the srx, its not what the factory designed the exh system for anyways.The viper was quite another story, it was a triple with a single pipe.