Is there a way to access System instances for a Scene or must System updates (e.g., change the culling distance of a System) always route through a Component?
Generally Systems are designed to operate on Entities (within Scenes) and their Components. Each System can be updated against multiple Scenes (and the Scene’s entities).
If you have state that you want to be represented with a System, one method to do that is to have a root entity that holds a “System component”.
There’s more information on System’s in last years WWDC session and on the developer documentation website: