### 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)

lcd.sh[j * 4 + 1] = src_capture[j].g;
						lcd.sh[j * 4 + 2] = src_capture[j].b;
						lcd.sh[j * 4 + 3] = src_capture[j].a;
					}
					flags |= INSTANCE_DATA_FLAG_USE_LIGHTMAP_CAPTURE;
					inst->gi_offset_cache = lightmap_captures_used;
					lightmap_captures_used++;
					uses_lightmap = true;
				}
			} else {
				if (p_using_opaque_gi) {
					flags |= INSTANCE_DATA_FLAG_USE_GI_BUFFERS;
				}
				if (inst->voxel_gi_instances[0].is_valid()) {
					uint32_t probe0_index = 0xFFFF;
					uint32_t probe1_index = 0xFFFF;
					for (uint32_t j = 0; j < scene_state.voxelgis_used; j++) {
						if (scene_state.voxelgi_ids[j] == inst->voxel_gi_instances[0]) {
							probe0_index = j;
						} else if (scene_state.voxelgi_ids[j] == inst->voxel_gi_instances[1]) {
							probe1_index = j;
						}
					}
					if (probe0_index == 0xFFFF && probe1_index != 0xFFFF) {
						
						SWAP(probe0_index, probe1_index);
					}
					inst->gi_offset_cache = probe0_index | (probe1_index << 16);
					flags |= INSTANCE_DATA_FLAG_USE_VOXEL_GI;
					uses_gi = true;