Ok, so I had time to double check the design again. I was hoping there wouldn't be anything major, but alas, I missed a couple of major stuff:

• Wrong footprint for the FAN48623. I initially used a 0.35 mm pitch footprint, but somehow missed in the datasheet that the part is 0.4 mm pitch.
• Incorrect pitch part for the battery and external DC terminal block. The mistake was from when the terminal block was originally going to be 5 mm pitch, but decided to use a 3.5 mm pitch one due to space constraints.

With these issues out of the way, I am now more comfortable placing the order for the first prototype units in the coming week. 

 Also, I designed the USB supply protection accessory that I mentioned:

This has the same ideal diode circuit as the one on the PowerUPS main board, and prevents the supply from being back-powered by PowerUPS. The supply goes on one end, and the cable to the Pi's USB port on  another. 

Again, this is so that the Pi's USB port can still be used with PowerUPS, *unlike* for other UPS's which asks the user to use the USB connector on the UPS instead. (PowerUPS doesn't even have a USB port on its own - though it can still take external DC sources like solar panels using a screw terminal block).