I have had problems in the past with Funcube dongles not being detected using CTT Sensorstations, just as with RPi based Sensorgnomes. But if I make sure the firmware is the 48KHz version (the same one you mentioned), the Funcubes work just fine. If you purchase your Funcubes from a second party seller (Compudata or RFS Scientific) they will have already updated the firmware to be the 48KHz version, and you would not have to do so.
Because the firmware update is fairly straightforward, I'd still say it's best practice to make sure your Funcubes have the correct firmware for use with a RPi based receiver (RPi based Sensorgnome and CTT Sensorstation). Failure to do so COULD result in nothing being detected by the antenna connected to that Funcube dongle!
I'd be happy to hear if CTT ensures that their stations have the ability to function with Funcubes no matter what firmware is on it, but I'm not sure that they do, and I'd hate to not collect any data by assuming they do!
Feel free to contact me if you would like instructions for how to update the firmware on Funcube dongles!
Matthew M Webb
Avian Ecologist and Motus WTS Coordinator, Full Annual Cycle Monitoring Program
Bird Conservancy of the Rockies
Motus project #281