Just to make sure that I let this get back to the community, here is a message I got from Federico after I asked him directly about controlling the Atheros processor.
I remember your post and I confirm what I've written that day: there's
no way to turn on the ar9331 one you turned it off. That would mean the
32u4 is using one or more pins to control something like a relay but
would mean losing those pins
I've also seen that post about the frequency and the intro "welcome
brave guys" makes me think it's something highly experimental
The 32u4 can indeed run without the atheros, but cannot turn it back on,
thus, once turned off, you'll end using a leonardo instead of a yun
PS: please, next time write directly on the forum since this kind on
knowledge is worth sharing with everybody
Of note, the scaling he (and I) was referring to is here (https://forum.openwrt.org/viewtopic.php?pid=178259#p178259) and is from 2012. I'm not sure what progress has been made since then (if at all).
Also of note, I think Federico had replied to a post by another person who asked the same question (which I found herehttp://forum.arduino.cc//index.php?topic=192413.0 - it looks like I'm not the only one that would love this).
I also found a post where some folks show some power savings using sleep mode http://forum.arduino.cc//index.php?topic=190441.0
Thank you to Federico and others for shedding some light on this.