### 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)

return 256;
}
RenderForwardMobile *RenderForwardMobile::singleton = nullptr;
void RenderForwardMobile::_update_shader_quality_settings() {
	Vector<RD::PipelineSpecializationConstant> spec_constants;
	RD::PipelineSpecializationConstant sc;
	sc.type = RD::PIPELINE_SPECIALIZATION_CONSTANT_TYPE_INT;
	sc.constant_id = SPEC_CONSTANT_SOFT_SHADOW_SAMPLES;
	sc.int_value = soft_shadow_samples_get();
	spec_constants.push_back(sc);
	sc.constant_id = SPEC_CONSTANT_PENUMBRA_SHADOW_SAMPLES;
	sc.int_value = penumbra_shadow_samples_get();
	spec_constants.push_back(sc);
	sc.constant_id = SPEC_CONSTANT_DIRECTIONAL_SOFT_SHADOW_SAMPLES;
	sc.int_value = directional_soft_shadow_samples_get();
	spec_constants.push_back(sc);
	sc.constant_id = SPEC_CONSTANT_DIRECTIONAL_PENUMBRA_SHADOW_SAMPLES;
	sc.int_value = directional_penumbra_shadow_samples_get();
	spec_constants.push_back(sc);
	sc.type = RD::PIPELINE_SPECIALIZATION_CONSTANT_TYPE_BOOL;
	sc.constant_id = SPEC_CONSTANT_DECAL_USE_MIPMAPS;
	sc.bool_value = decals_get_filter() == RS::DECAL_FILTER_NEAREST_MIPMAPS ||
			decals_get_filter() == RS::DECAL_FILTER_LINEAR_MIPMAPS ||
			decals_get_filter() == RS::DECAL_FILTER_NEAREST_MIPMAPS_ANISOTROPIC ||
			decals_get_filter() == RS::DECAL_FILTER_LINEAR_MIPMAPS_ANISOTROPIC;
	spec_constants.push_back(sc);
	sc.constant_id = SPEC_CONSTANT_PROJECTOR_USE_MIPMAPS;
	sc.bool_value = light_projectors_get_filter() == RS::LIGHT_PROJECTOR_FILTER_NEAREST_MIPMAPS ||
			light_projectors_get_filter() == RS::LIGHT_PROJECTOR_FILTER_LINEAR_MIPMAPS ||