That is my understanding as well. The reason the FF&C clause was not used was because instead, Taney argued that neither the feds nor any state could prohibit slavery. That was grossly inaccurate. Until the 13th -15th Amendments, slavery was an issue of each sovereign state.
I think FF&C probably would have been effective in this case as even just recently, Congress had to pass DOMA to prevent FF&C from operating in gay marriage issues between states.
FF&C has had little application over time.