Good analysis and you have made some valid points about the breakout board's power circuitry. I have both boards, Arduino and Mini breakout, and was surprised to discover that part of the power circuitry is pretty much identical between the two boards, some of which seems redundant on the mini breakout. It seems like it could have been handled a little simpler. After all, the Edison module itself only needs a single voltage between 3.15V and 4.4V to do everything it does. Either a standard 3.3V source or a 3.7V battery level works nicely.
The Arduino breakout does need some of this complexity due to handling both 3.3V and 5V Arduino shields. Maybe Intel developed the Mini breakout after the Arduino breakout and just reused the same circuitry?
BTW, the Arduino breakout does have the battery pins marked plus and minus. Too bad the Mini doesn't. In fact, the Arduino board has all the components labeled. A diode could also avoid the problem of reversing the battery leads.
