A lot more going on here than you think. A few things to start with:
Scavenging relates to the low pressure cause by the passing exhaust of the opposing order cylinder drawing the exhaust out of the next cylinder as the valve opens which assists in reducing the pressure in the cylinder and increasing the intake flow. This is why different length headers will affect different power bands, they can only ever be tuned for a small band. Unless this WRX has a "tuned" manifold, it's unlikely to have any scavenging as the cylinders are firing in close succession (1,2...3,4) this is where the distinctive burble comes from. There is always an exhaust overlap on the paired cylinders. Providing the exhaust isn't completely wrong, this has little effect on FI engines as the FI is creating more force than scavenging can. Tuned turbo exhausts are different, they're designed for flow and velocity purposes. Superchargers are different again, they're designed to unify the pulses at an appropriate point.
Essentially the most important aim point for any exhaust is to have a tuned termination point; a point at which the exhaust increases in volume significantly enough to act in effect, the end of the exhaust, in terms of what the engines "sees". This point relates to engine size, power, flow, NA super or turbo charged; It can be calculated but its more trial and error and for over all performance is reflected by the position of the resonator (it's primary function). Basically this process is to collect the pulses into a unified flow otherwise (as far as I understand it) the exhaust is constantly fighting high and low pressure. From here you can reduce the exhaust diameter as desired or delete the rest all together. In the case of turbo chargers, the turbo is this point. The dump pipe then allows this high volume, unified exhaust to flow freely from the turbo without restriction, backing up and slowing the turbo, to the first muffler.
The next consideration is maintaining exhaust temperature. Cold air moves slower, you want the exhaust to stay hot. When you have a long exhaust the temp is going to drop, this is where a volume change comes in. By reducing the diameter it maintains constant velocity through maintaining temp and pressure. If you don't reduce the diameter you risk the exhaust slowing down and causing back pressure (back pressure is bad); Though, in street applications, the volume of the muffler will buffer back pressure here so its not essential to get perfect.
Basically this all works out organically when you run headers into a cat and muffler in an NA SW20 or AW11. You'd punish yourself with a strait through following the same path as stock. The ideal length to the termination point on an AW11 is about 50cm shorter than the stock path, thats why I looped around the exhaust and added a hot dog (resonator) to create a shorter termination but overall longer. This also brings the last consideration (which is limited on MR2's) noise attenuation.
As above mufflers are important to help the exhaust flow, but too big or too convoluted will cause restriction. The simplest way to quieten an exhaust is length. The longer the exhaust the quieter it is.
This all becomes a balancing act and with some creative thinking you can be quiet flexible with the way you approach the problem: longer with less restrictive mufflers but changes in diameter, shorter with baffled mufflers, hot dogs, resonators, resonator cavities, balance weights. The options are huge but for street applications it all becomes very academic and as I said, it basically all happens organically in the SW20.