### Godot version

v4.1.dev4.mono.official [5c2295ff5]

### System information

Godot v4.1.dev4.mono - Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti with Max-Q Design (NVIDIA; 31.0.15.3179) - Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz (12 Threads)

### Issue description

When I open my project console gets filled with these errors.

```
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
```
### Steps to reproduce (from fresh new project)
Steps to reproduce `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` error.
1. Create new project.
1.1 Godot version used: v4.1.beta2.mono.official [a2575cba4]).
1.2 I have this setting On: Editor -> Editor Settings -> General -> Interface -> Scene Tabs -> "Restore Scenes On Load".
2. Copy/Paste .glb model with a skeleton to the project folder.
3. Double click .glb file in the editor and click Reimport.
4. Right click .glb file and select New Inherited Scene.
5. Click ctrl+s to save that scene for example player.tscn.
6. Right click player.tscn and select Instantiate.
7. Save everything and restart Godot editor. When launching editor you will see message `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` in console and Output.

### Steps to reproduce (from MRP)

Open project

### Minimal reproduction project

MRP uses v4.1.beta1.mono.official [828ec2c5d], but same error still persists
[MRP.zip](https://github.com/godotengine/godot/files/11703993/MRP.zip)

RD::get_singleton()->draw_command_begin_label("Shadow Render");
	for (SceneState::ShadowPass &shadow_pass : scene_state.shadow_passes) {
		RenderListParameters render_list_parameters(render_list[RENDER_LIST_SECONDARY].elements.ptr() + shadow_pass.element_from, render_list[RENDER_LIST_SECONDARY].element_info.ptr() + shadow_pass.element_from, shadow_pass.element_count, shadow_pass.flip_cull, shadow_pass.pass_mode, 0, true, false, shadow_pass.rp_uniform_set, false, Vector2(), shadow_pass.lod_distance_multiplier, shadow_pass.screen_mesh_lod_threshold, 1, shadow_pass.element_from, RD::BARRIER_MASK_NO_BARRIER);
		_render_list_with_threads(&render_list_parameters, shadow_pass.framebuffer, RD::INITIAL_ACTION_DROP, RD::FINAL_ACTION_DISCARD, shadow_pass.initial_depth_action, shadow_pass.final_depth_action, Vector<Color>(), 1.0, 0, shadow_pass.rect);
	}
	if (p_barrier != RD::BARRIER_MASK_NO_BARRIER) {
		RD::get_singleton()->barrier(RD::BARRIER_MASK_RASTER, p_barrier);
	}
	RD::get_singleton()->draw_command_end_label();
}
void RenderForwardClustered::_render_particle_collider_heightfield(RID p_fb, const Transform3D &p_cam_transform, const Projection &p_cam_projection, const PagedArray<RenderGeometryInstance *> &p_instances) {
	RENDER_TIMESTAMP("Setup GPUParticlesCollisionHeightField3D");
	RD::get_singleton()->draw_command_begin_label("Render Collider Heightfield");
	RenderSceneDataRD scene_data;
	scene_data.cam_projection = p_cam_projection;
	scene_data.cam_transform = p_cam_transform;
	scene_data.view_projection[0] = p_cam_projection;
	scene_data.z_near = 0.0;
	scene_data.z_far = p_cam_projection.get_z_far();
	scene_data.dual_paraboloid_side = 0;
	scene_data.opaque_prepass_threshold = 0.0;
	scene_data.time = time;
	scene_data.time_step = time_step;
	RenderDataRD render_data;
	render_data.scene_data = &scene_data;
	render_data.cluster_size = 1;