Instanced .tscn has no CollisionShape3D resources when loaded via ResourceLoader.load_threaded_request()

[PunkSolar]

Describe the bug

Attempted to switch over a 3D project from JoltPhysics3D to RapierPhysics3D v0.35.2, but when testing the new physics engine through my project's main menu and loading screen, the 'game' scene - when instantiated - has no collision data and instead reports the following two errors for each CollisionShape3D resource in the instantiated scene:

E 0:00:02:389   godot_core::private::install_godot_rust_hook::{{closure}}: [panic /home/runner/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/godot-ffi-0.5.5/src/binding/single_threaded.rs:140]  attempted to access binding from different thread than main thread; this is UB - use the "experimental-threads" feature.
  <C++ Source>  /home/runner/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/godot-core-0.5.5/src/private.rs:331 @ godot_core::private::install_godot_rust_hook::{{closure}}()

E 0:00:02:397   scene_manager.gd:26 @ deferred_load_scene(): Invalid shape id
  <C++ Source>  src/servers/rapier_physics_server_impl.rs:226 @ godot_rapier::servers::rapier_physics_server_impl::RapierPhysicsServerImpl::shape_set_data()
  <Stack Trace> scene_manager.gd:26 @ deferred_load_scene()

To Reproduce

Steps to reproduce the behavior:

1. Ensure that the 3D physics engine is set to Jolt3D
2. Load the demo scene directly via the Godot Editor's 'Run Current Scene' button.
3. Load the demo scene by pressing 'Run Main Scene' and clicking the 'load demo scene' button
4. Install the v0.35.2 RapierPhysics3D add-on
5. Switch to Rapier3D
6. Repeat step 2; Note that nothing has changed.
7. Repeat step 3; Note that the rigidbodies fall through the floor, and that there is exactly ten errors reported each time.

Expected behavior

After switching to Rapier3D, all the physics objects should be working as they would in Jolt3D: PhysicsObject3D and CollisionObject3D nodes should have their collision data loaded properly.

Environment:

• OS: Kubuntu 26.04
• Version: v0.35.2
• Godot Version: v4.7
• Type: Single player 3D

Example project(zip)

issue_example_project_2026-08-17_19-50-28.zip

[PunkSolar]

Originally this was just going to be titled 'Instanced .tscn file has no collisiondata', but after a discovery I made during the creation of the example project that I am almost certain that that's the root cause.

[Ughuuu]

I wonder what should happen with this. Is it a godot-rust bug? Is it a godot bug? Should godot call me from main thread? How does Jolt do it, as this is in theory undefined behaviour? Do they have a lock/mutex in front? And how do they know if/when to add the lock.