In the rules for the Quest Enemy and Quest Shadow tokens (section 15.4) it has soothing like “Note: This Shadow becomes part of the reserve only when directly (or expressly) indicated.”
Since the Quest setup indicates what specific Shadow tokens to put in the Shadow Reserve is this actually any different than how all the other Shadow tokens are handled?
Yes, these 2 tokens are for specific situations described in the story book & book of secrets. So the game will tell you when to shuffle them to the reserve (story book) and how to handle them when revealed (book of secrets).
The standard shadow tokens just represent spawning indicated enemy(ies).