Is the SAMD11_RX getting power in the the ATSAM from the MG24 TX pin ? And then bleeding power out via the regulator to the charger IC ? I measure 3v51 on the Vin pin before connecting USB and 3v47 after disconnecting.
LED is flashing bright orange while connected and dim after disconnecting, it goes off after a power cycle. Without Serial the Vin pin measures the same as the battery.
So the MG24 TX will need to be open collector with a pullup to prevent this issue. Connecting U10 to VIN instead of VBUS might help but might also mess up USB state machines.