### 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)

ERR_FAIL_COND(p_render_buffers.is_null());
	Ref<RenderBufferDataForwardClustered> rb_data = p_render_buffers->get_custom_data(RB_SCOPE_FORWARD_CLUSTERED);
	ERR_FAIL_COND(rb_data.is_null());
	ERR_FAIL_COND(!p_render_buffers->has_custom_data(RB_SCOPE_GI));
	Ref<RendererRD::GI::RenderBuffersGI> rbgi = p_render_buffers->get_custom_data(RB_SCOPE_GI);
	Ref<RendererRD::GI::SDFGI> sdfgi;
	if (p_render_buffers->has_custom_data(RB_SCOPE_SDFGI)) {
		sdfgi = p_render_buffers->get_custom_data(RB_SCOPE_SDFGI);
	}
	Size2i size = p_render_buffers->get_internal_size();
	float ratio = float(size.x) / float((size.x + size.y) / 2);
	uint32_t target_width = uint32_t(float(get_volumetric_fog_size()) * ratio);
	uint32_t target_height = uint32_t(float(get_volumetric_fog_size()) / ratio);
	if (p_render_buffers->has_custom_data(RB_SCOPE_FOG)) {
		Ref<RendererRD::Fog::VolumetricFog> fog = p_render_buffers->get_custom_data(RB_SCOPE_FOG);
		
		if (p_environment.is_null() || !environment_get_volumetric_fog_enabled(p_environment) || fog->width != target_width || fog->height != target_height || fog->depth != get_volumetric_fog_depth()) {
			p_render_buffers->set_custom_data(RB_SCOPE_FOG, Ref<RenderBufferCustomDataRD>());
		}
	}
	if (p_environment.is_null() || !environment_get_volumetric_fog_enabled(p_environment)) {
		
		return;
	}
	if (p_environment.is_valid() && environment_get_volumetric_fog_enabled(p_environment) && !p_render_buffers->has_custom_data(RB_SCOPE_FOG)) {
		
		Ref<RendererRD::Fog::VolumetricFog> fog;