Perhaps it was just me being gullible, but when reading out each scenario I was under the impression that the game was introducing special storm or bird flock mechanics into certain scenarios when, in actuality, all that changes are that mission's objectives with some cute flavor text to justify them.
You haven't been misled. We are indeed adding special events to the stage mode. You will see the relevant updates in the next 1 to 2 weeks, including 3 types of unexpected situations