Here's the deal......
PISTON GOES UP: That draws air/fuel into the lower half.
PISTON GOES DOWN: the intake valve closes. as the piston goes down, it compresses the charge in the lower. Eventually... the exhaust port opens first, and that relives the cyl pressure. Then the "Bypass" ports open. Since the lower is now under pressure (about 5~7psi) It's pushed into the cyl, and forces out the rest of the exhaust.
So... there is a lot less mixing of exhaust gases than you would think.
This is also why we watch compression closer than a 4-stroke. When the rings start to leak down... you displace the fresh charge coming in.. and the engine goes lean. Couple that with the heat generated... and the engine will quickly eat itself.
Some of the fresh charge is lost into the exhaust, and the sonic wave produced in the cone pipe pushes that charge back into the cylinder. Also, as the charge is delivered to the cylinder, the goal is to have it directed to the top of the cylinder to displace the spent charge as it leaves the exhaust port without loosing the fresh charge out of the exhaust port.
There's an art to getting it all right and balanced, timed, etc. port size, timing, location, all involved, along with sonic/harmonic length of cone pipe which on the skis is adjusted by the amount of water in the pipe, etc.
Unfortunately, in order for them to run correctly, both unburned oil and fuel are still lost to the exhaust, which presents a huge problem in terms of meeting EPA requirements.
The BRP E-TEC, wow, those things are IMO nothing short of incredible engines, took a lot of effort to get there, a road full of pot holes.
So much of the cool old 2 stroke stuff has disappeared, such as the aquascooter. (Can't believe I just posted that!)
http://en.wikipedia.org/wiki/Aqua_scooter
Not that anything will ever come of it, but what do you guys think of a rotary engine powered surfboard that "meets EPA requirements"?
http://www.deckjetwatercraft.com/xboard/