Looking at it again, I think it uses PWM from pin 14 of the MCU to control the input power. That sounds reasonable. I would need to fire up my scope to prove it. However, the scope is not working very well. I think it may need a firmware upgrade.
It may not do anything much other than idle until it recognises the battery type and required voltage from the NTC, COP and battery voltage, then presumably tries to maintain an appropriate constant voltage - with no current limiting?? I think NTC may go to a thermistor inside the battery that has a negative coefficient.
What type of batteries is this for - NiCd / NiMH, at a guess? It is a Li-ion battery.
Also can you double check the 100n cap connection - does it really go to pin 3? You're right. It & the 47 k go to pin 5. I must have counted from the wrong end when looking at the copper side of the PCB. The MCU in the data should only have a resistor on that pin.