I think it works as you said.
Other devices having FCCU has either dedicated EOUT outputs and EIN inputs, or it does not have FCCU external inputs at all.
Here it is implemented differently, it uses EOUT as bi-directional I/Os what means it works simultaneously
“The FCCU provides up to two bidirectional signals (EOUT interface) as a failure indication to the external world. These signals need to be mapped to appropriate pins for external visibility. Since SIUL2 does not control the pad buffer enable during Alternate function, FCCU provides a mechanism to drive the pad in OD (Open Drain) mode where the pad is driven Hi-Z only when FCCU drives logic '1' else it drives logic '0' (when FCCU drives logic '0'). The selection to OD is done by OD bit in FCCU_CFG register.”
Due to that I suppose there is expected is either compounded function with open-drain where either ends may report faults over FI[0] pad. It means input buffers are always active even for output functionality with push-pull drivers. In my opinion it is just needed to ignore NCF54 (do not set any reaction) if you don’t use FI[0] pin as input.