@ckuehnel Did you ever figure this out? I just got my 18650 hat. I took it apart and also don't see any control circuitry. I'm now guessing that the USB connector on the hat simply feeds into the 5V input of the M5StickC, and the AXP192 inside the M5StickC controls the charge of the 18650 cell. There is some info in the AXP192 data sheet about a back-up battery, but it's been a while since I read it, and I'm not sure it's relevant.
One interesting thing ... I'm working on a project where I turn the display off after a few seconds if the M5StickC is not plugged in. Either by shrewd design or by my dumb luck, that works when the M5StickC is on the hat. ("It works" means the display turns off after a few seconds.)