### 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)

fb_size.x = p_size[right_axis];
		fb_size.y = p_size[up_axis];
		scene_data.cam_transform.origin = center + axis * half_size;
		scene_data.cam_transform.basis.set_column(0, right);
		scene_data.cam_transform.basis.set_column(1, up);
		scene_data.cam_transform.basis.set_column(2, axis);
		
		float h_size = half_size[right_axis];
		float v_size = half_size[up_axis];
		float d_size = half_size[i] * 2.0;
		scene_data.cam_projection.set_orthogonal(-h_size, h_size, -v_size, v_size, 0, d_size);
		
		Transform3D to_bounds;
		to_bounds.origin = p_bounds.position;
		to_bounds.basis.scale(p_bounds.size);
		RendererRD::MaterialStorage::store_transform(to_bounds.affine_inverse() * scene_data.cam_transform, scene_state.ubo.sdf_to_bounds);
		scene_data.emissive_exposure_normalization = p_exposure_normalization;
		_setup_environment(&render_data, true, Vector2(1, 1), false, Color());
		RID rp_uniform_set = _setup_sdfgi_render_pass_uniform_set(p_albedo_texture, p_emission_texture, p_emission_aniso_texture, p_geom_facing_texture);
		HashMap<Size2i, RID>::Iterator E = sdfgi_framebuffer_size_cache.find(fb_size);
		if (!E) {
			RID fb = RD::get_singleton()->framebuffer_create_empty(fb_size);
			E = sdfgi_framebuffer_size_cache.insert(fb_size, fb);
		}
		RenderListParameters render_list_params(render_list[RENDER_LIST_SECONDARY].elements.ptr(), render_list[RENDER_LIST_SECONDARY].element_info.ptr(), render_list[RENDER_LIST_SECONDARY].elements.size(), true, pass_mode, 0, true, false, rp_uniform_set, false);
		_render_list_with_threads(&render_list_params, E->value, RD::INITIAL_ACTION_DROP, RD::FINAL_ACTION_DISCARD, RD::INITIAL_ACTION_DROP, RD::FINAL_ACTION_DISCARD, Vector<Color>(), 1.0, 0, Rect2(), sbs);
	}
	RD::get_singleton()->draw_command_end_label();
}
void RenderForwardClustered::base_uniforms_changed() {