@hamishwillee I just saw that the documentation states that:
The recommended mode for autotuning is Altitude mode , but any other flight mode can be used. During auto tuning, the RC sticks can still be used to fly the vehicle.
This is not correct, moving the sticks while using the autotune for multirotors with immediately interrupt the autotune procedure. @MBicer This is the reason why it fails all the time for you.