This only affects NPC's during the end-state of their corresponding town.
They're already changing positions during the town's story.
And the time of day is already changing each time the player get an ability, so their changing positions MIGHT already seem to match up?

Hint NPC's are not affected by time of day, because they appear after you get a new ability, so they DEFINITELY already change position at the same time a new ability is acquired + daytime changes.

start_state
mid_state
end_state_day
end_state_evening
end_state_night