### 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)

#ifdef DEBUG_ENABLED
			}
#endif
			mesh_surface = surf->surface;
		}
		if (!mesh_surface) {
			continue;
		}
		
		if (shader->uses_time) {
			should_request_redraw = true;
		}
		
		SceneShaderForwardClustered::ShaderData::CullVariant cull_variant;
		if (p_pass_mode == PASS_MODE_DEPTH_MATERIAL || p_pass_mode == PASS_MODE_SDF || ((p_pass_mode == PASS_MODE_SHADOW || p_pass_mode == PASS_MODE_SHADOW_DP) && surf->flags & GeometryInstanceSurfaceDataCache::FLAG_USES_DOUBLE_SIDED_SHADOWS)) {
			cull_variant = SceneShaderForwardClustered::ShaderData::CULL_VARIANT_DOUBLE_SIDED;
		} else {
			bool mirror = surf->owner->mirror;
			if (p_params->reverse_cull) {
				mirror = !mirror;
			}
			cull_variant = mirror ? SceneShaderForwardClustered::ShaderData::CULL_VARIANT_REVERSED : SceneShaderForwardClustered::ShaderData::CULL_VARIANT_NORMAL;
		}
		RS::PrimitiveType primitive = surf->primitive;
		RID xforms_uniform_set = surf->owner->transforms_uniform_set;
		SceneShaderForwardClustered::PipelineVersion pipeline_version = SceneShaderForwardClustered::PIPELINE_VERSION_MAX; 
		uint32_t pipeline_color_pass_flags = 0;
		uint32_t pipeline_specialization = 0;
		if constexpr (p_pass_mode == PASS_MODE_COLOR) {
			if (element_info.uses_softshadow) {