Does your device have a power light?
Why not just use the 78732, open drain output. Connect them both to a single LED and single resistor. Two components. When the LED is lit, one or both are charging. When it's out, charging is done. As long as there's some other indicator light when plugged in, you will know the USB power is good. And therefore, if the LED is off, both batteries are finished charging.
I'm all about simple. Heck, give them each their own LED and resistor and add a dedicated Vusb LED and resistor. That's 3 LED and 3 resistors, and you are still ahead of the curve. Wash on parts counts, but fewer pads and much simpler routing.