### 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)

sdfgi = gi.create_sdfgi(p_environment, p_world_position, requested_history_size);
		rb->set_custom_data(RB_SCOPE_SDFGI, sdfgi);
	} else {
		
		sdfgi->update(p_environment, p_world_position);
	}
}
int RenderForwardClustered::sdfgi_get_pending_region_count(const Ref<RenderSceneBuffers> &p_render_buffers) const {
	Ref<RenderSceneBuffersRD> rb = p_render_buffers;
	ERR_FAIL_COND_V(rb.is_null(), 0);
	if (!rb->has_custom_data(RB_SCOPE_SDFGI)) {
		return 0;
	}
	Ref<RendererRD::GI::SDFGI> sdfgi = rb->get_custom_data(RB_SCOPE_SDFGI);
	int dirty_count = 0;
	for (const RendererRD::GI::SDFGI::Cascade &c : sdfgi->cascades) {
		if (c.dirty_regions == RendererRD::GI::SDFGI::Cascade::DIRTY_ALL) {
			dirty_count++;
		} else {
			for (int j = 0; j < 3; j++) {
				if (c.dirty_regions[j] != 0) {
					dirty_count++;
				}
			}
		}
	}
	return dirty_count;
}
AABB RenderForwardClustered::sdfgi_get_pending_region_bounds(const Ref<RenderSceneBuffers> &p_render_buffers, int p_region) const {