### 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)

uint32_t shadow_pass_index = scene_state.shadow_passes.size();
	SceneState::ShadowPass shadow_pass;
	RenderSceneDataRD scene_data;
	scene_data.cam_projection = p_projection;
	scene_data.cam_transform = p_transform;
	scene_data.view_projection[0] = p_projection;
	scene_data.z_far = p_zfar;
	scene_data.z_near = 0.0;
	scene_data.lod_distance_multiplier = p_lod_distance_multiplier;
	scene_data.dual_paraboloid_side = p_use_dp_flip ? -1 : 1;
	scene_data.opaque_prepass_threshold = 0.1f;
	scene_data.time = time;
	scene_data.time_step = time_step;
	RenderDataRD render_data;
	render_data.scene_data = &scene_data;
	render_data.cluster_size = 1;
	render_data.cluster_max_elements = 32;
	render_data.instances = &p_instances;
	render_data.render_info = p_render_info;
	_setup_environment(&render_data, true, Vector2(1, 1), !p_flip_y, Color(), false, p_use_pancake, shadow_pass_index);
	if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_DISABLE_LOD) {
		scene_data.screen_mesh_lod_threshold = 0.0;
	} else {
		scene_data.screen_mesh_lod_threshold = p_screen_mesh_lod_threshold;
	}
	PassMode pass_mode = p_use_dp ? PASS_MODE_SHADOW_DP : PASS_MODE_SHADOW;