Hi Slimfish,
I am not sure I understand your point.
With the minimum USB voltage of 4.5 V, the output to power switch is well over 4 V, allowing adequate margin for the 3.6V supply and the two regulator ICs:XC6206P302 and XC6206P332.
When operating from the battery, as long as there is more than 3.0V from the battery, all should be good. The 3.3 V regulator would not be regulating, but the 3.0V battery voltage will still pass through. The ST uController operates at 3V. The only use for the 3.3 V is the SD card. Many SD cards will work at 3.0 V, but many will not.
The 3.6V is used for the +/- 5V supply boost regulator SP3232. This, unlike many switched capacitor power circuits, has regulated outputs, regardless if the actual input voltage. I think using this IC is a bit of genius on the part of SeeedStudio. It is also the output buffer for the test signal, with a guaranteed rise and fall time into high capacitance loads.
Most importantly, if you want to discharge the battery to near 3.0 Volts, it will have a significantly shorter life.
Shazam