I haven't seen anything in the PMIC Datasheet that would suggest this.....but I could be missing something.
I tried to reproduce your issue, and can now confirm something is very strange.
My Test:
3xAA (L91's) Resting Voltage = 5.08 V
3xAA Operating Voltage = 4.91 V at 13 mA (Cloud Connected, powered by 3xAA only on Li-Po connector)
Then Connecting a 5.25V Power Supply to the Boron USB connector actually INCREASED the current leaving the 3xAA to 41 mA. Approximately 140 mW was un-accounted for. 1 Hz pattern on Charger LED. Test Stopped immediately. I used 5.25 V to be above the Boost Mode Voltage of 5.12V (Votg).
Repeated with 5.00V Power Supply to the Boron USB, same results.
Something is going wrong.
I don't think you are technically doing anything Out-Of-Spec for the PMIC, but this does deviate from the Intended Operation of a Li-Po charger IC.
Someone might be able to recommend a simple power switch IC that will perform the UPS duty external to the Boron ?