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"
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.
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
