Quick note on power rail protection. LTC4365 (pdf, digikey) seems nice little device for protecting things; it does under- and over-voltage, and reverse polarity protection. It is bit pricey though, but if that avoids setting things on fire then I think its still worth it. Needs to be paired with dual MOSFET, digikey has plenty of options available. DMG9926 (pdf, digikey) was one of the cheapest. Some never-heard company "Taiwan Semiconductor" had parts (pdf) specifically designed for Li-ion battery packs, that included also ESD protection which might be nice?

Did the math on the resistor values for LTC4365, and 2.49M - 249k - 249k will produce exactly 3V/6V thresholds with <5mV offset and 1-2 µA current draw. Seems good, 249 being on the E48 series and readily available as 1% SMD resistor.

Biggest problem (in addition to cost) might be fitting two chips and handful of passives to the board. We'll see how it goes..