I think grouping scenes will be a great way to organize work and make checking for specific scenes easier.
so this is how it will work.
when adding a new layer it will ask you either add a scene or a group like this:
and this is how an example of the folders wil look like (screenshot from rpg maker MV)
after a person adds a group they can check if a scene is in a specific group.
so for example, if the player is in a bonus room the game will stop checking for health.