### 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)

light_projectors_get_filter() == RS::LIGHT_PROJECTOR_FILTER_NEAREST_MIPMAPS_ANISOTROPIC ||
			light_projectors_get_filter() == RS::LIGHT_PROJECTOR_FILTER_LINEAR_MIPMAPS_ANISOTROPIC;
	spec_constants.push_back(sc);
	scene_shader.set_default_specialization_constants(spec_constants);
	base_uniforms_changed(); 
}
RenderForwardMobile::RenderForwardMobile() {
	singleton = this;
	sky.set_texture_format(_render_buffers_get_color_format());
	String defines;
	defines += "\n#define MAX_ROUGHNESS_LOD " + itos(get_roughness_layers() - 1) + ".0\n";
	if (is_using_radiance_cubemap_array()) {
		defines += "\n#define USE_RADIANCE_CUBEMAP_ARRAY \n";
	}
	
	defines += "\n#define MAX_DIRECTIONAL_LIGHT_DATA_STRUCTS " + itos(MAX_DIRECTIONAL_LIGHTS) + "\n";
	{
		
		scene_state.max_lightmaps = 2;
		defines += "\n#define MAX_LIGHTMAP_TEXTURES " + itos(scene_state.max_lightmaps) + "\n";
		defines += "\n#define MAX_LIGHTMAPS " + itos(scene_state.max_lightmaps) + "\n";
		scene_state.lightmap_buffer = RD::get_singleton()->storage_buffer_create(sizeof(LightmapData) * scene_state.max_lightmaps);
	}
	{
		
		scene_state.max_lightmap_captures = 2048;
		scene_state.lightmap_captures = memnew_arr(LightmapCaptureData, scene_state.max_lightmap_captures);
		scene_state.lightmap_capture_buffer = RD::get_singleton()->storage_buffer_create(sizeof(LightmapCaptureData) * scene_state.max_lightmap_captures);
	}
	{