Understandable why you focus on the engine, and not making a game.
Sounds like a great plan with a licensed engine with free non-commercial use!
Are you switching out the entire scene, or unloading/loading assets into a single scene?
My project has XR as a focus, and I ran into the problem of staying in XR mode when switching scenes.
I ended up using a single scene and loading/unloading assets as needed.
See more here WebXR across multiple scenes - #5 by Basic
Your sector-management (spatial partitioning) is a great idea too to keep the scene performant 
Does your projectiles and the player also use the same sector-management?