HI Jooo
My guess is that the Furuta Pendulum is fully controllable when the input is the torque, and not the underlying DC motor characteristics.
If you replace the entire motor with a direct torque input, the system is controllable and the controllability matrix has rank 4:
At the same time if you use the simplified DC motor model current is linearly related to torque, so if you feed a current sources to the motor (instead of voltage) you get as well a fully controllable system:
I may be wrong, but I don't think you can get a proper controllability matrix if you include two cascading system (external loop: arm position, internal loop: DC motor torque) as both open loop, like you were doing. You need to examine both system independently, the position loop assuming a perfect dc motor (eg torque (or current) fully controllable)
Hope this sparks some thoughts - it has been many years since my control system lectures so take everything with a grain of salt.
Thanks
Vasco