Both herb gathering and mineral gathering have different effects if you play them after overwhelming darkness.
How do they interact with the forest gate?
I can see two arguments
1) you did not pass overwhelming darkness so no bonuses
2) if you pass the forest gate then you have passed the overwhelming darkness space, you were just told to use a different story event, so you do get the bonuses.
Which is right?
The Flower Knight's general rules say "The [Overwhelming Darkness] space retains all of its normal rules and cannot be skipped or ignored."
So, yeah, I think the answer is number 2: you treat that space like Overwhelming Darkness insofar as other rules are concerned.