Well, you seem to be a thorough person and if you want to know answers to these questions, I recommend reading some 2 stroke history: http://www.amrca.com/tech/tuners.pdf
In simplest terms I can make: the exhaust port is open for a duration and the transfer ports are flowing mixture into the combustion chamber. At the same time, a precise anount of back-pressure cushions this flow from excessively traveling out the exhaust port. The expansion chamber pipes use this dynamic event to both pull more mixture through the transfer ports and into the exhaust, then have a tuned reflection wave that forces it back into the chamber right before the exhaust port closes.
Since your stock exhaust has no way to produce the same effect, your best hope is to reduce back pressure a little and allow better scavenging of the exhaust gases without blowing your mixture charge into the pipe. There’s a limit.