Yes, the RTC in the AirSTORM-Y PMIC is functional. You can connect a backup battery to pin 52 on connector J1. 

On the Gumstix Tobi board (https://store.gumstix.com/tobi.html), I've tested the RTC using one of these: https://www.digikey.com/products/en?keywords=ML-621S%2FZTN

To read the RTC clock, you can use the linux userspace command: "sudo hwclock -r"

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https://www.gumstix.com/images/overo_signals_latest.pdf

Looking at page 7, the Signal "VBACKUP" is what you're interested in - although, I agree, it's not made that clear it can be used for the RTC backup battery. Rest assured, it can be.

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And just to be clear, J1 Pin 52 is directly connected to ball "M14", Signal "BKBAT" on the TPS65950.

http://www.ti.com/lit/ds/symlink/tps65950.pdf