I am not sure of your workflow, nor familiar with SWS or xenakios, so this may not be relevent.
I suspect people (mainly MixPre users) use Waveagent to split their polywav because they don't know about Reaper's explode item, or aren't using Reaper. Also, Waveagent does not work with 32bit-float. I work 24 bit, and do both methods, but Reaper's explode item is quick and easy. It also appears to duplicate the audio data for each exploded track of the polywav, and in the case of Mac, seems to throw the files into my Documents folder. I move them to the root Reaper folder of my project, so everything is together when I copy the folder for archiving or working from another machine.
Once exploded, all of the polywav tracks are separate (subtracks?) and I mix like any multitrack project. If I recorded L/R mix in the polywav (1-2), I just mute or delete them as I usually don't need them in a remix.