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I don't mind a mildly shorter-than-advertised battery life
It is hard to estimate but both features are more important when you e.g. run nrf52 based sensor for months from CR2032 battery (or years from bigger battery). With Bangle that is used daily and charged every week or two it may not make practical difference. That's why these are optional in the reference circuit.
Internal DC/DC when enabled is automatically turned on when the CPU itself draws high current (in mA) and is turned off when it draws uA because at low currents it does not help and possibly make things even worse. With other nrf52840 board I measured that when connected over BLE and running busy loop the CPU was drawing 9 mA from battery when DC/DC is disabled but only 6 mA when enabled. This may look nice but such savings only affect CPU itself, not display or GPS or HR or motion sensors. And most of the time the CPU is sleeping anyway => DC/DC is not helping.
External 32kHz crystal is supposed to be more accurate than internal 32kHz clock source and is not so sensitive to temperature changes. When it is not present the Bluetooth stack is configured to have larger tolerances to clock drift so the radio is woken up for slightly longer time to not miss data from other devices and also the internal 32kHz clock must be periodically recalibrated so the CPU is waking up to do this. However in reality the effect on battery life of Bangle 2 is again hardly noticeable. So it makes sense to enable these features when we know the watch has the components inside and it definitely saves some battery, but not much.
So IMO the real issue is a need for custom build and the uncertainty why your watch is different and what else can be wrong with it.
Thanks for the thorough explanation! I am going to test drive it this week and if I'm having any issue with it I'll reach out to Gordon when he's back in office. I don't mind a mildly shorter-than-advertised battery life; my old watch was only four days or so, so if it's that or better I think I'm good. It was purchased from adafruit if that makes any difference, not sure if going through a particular seller tends to have more issues than another or something.