### 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)

if (current_cluster_builder != nullptr) {
		current_cluster_builder->add_light(p_type == RS::LIGHT_SPOT ? ClusterBuilderRD::LIGHT_TYPE_SPOT : ClusterBuilderRD::LIGHT_TYPE_OMNI, p_transform, p_radius, p_spot_aperture);
	}
}
void RenderForwardClustered::setup_added_decal(const Transform3D &p_transform, const Vector3 &p_half_size) {
	if (current_cluster_builder != nullptr) {
		current_cluster_builder->add_box(ClusterBuilderRD::BOX_TYPE_DECAL, p_transform, p_half_size);
	}
}
void RenderForwardClustered::_process_ssao(Ref<RenderSceneBuffersRD> p_render_buffers, RID p_environment, const RID *p_normal_buffers, const Projection *p_projections) {
	ERR_FAIL_NULL(ss_effects);
	ERR_FAIL_COND(p_render_buffers.is_null());
	ERR_FAIL_COND(p_environment.is_null());
	Ref<RenderBufferDataForwardClustered> rb_data = p_render_buffers->get_custom_data(RB_SCOPE_FORWARD_CLUSTERED);
	ERR_FAIL_COND(rb_data.is_null());
	RENDER_TIMESTAMP("Process SSAO");
	RendererRD::SSEffects::SSAOSettings settings;
	settings.radius = environment_get_ssao_radius(p_environment);
	settings.intensity = environment_get_ssao_intensity(p_environment);
	settings.power = environment_get_ssao_power(p_environment);
	settings.detail = environment_get_ssao_detail(p_environment);
	settings.horizon = environment_get_ssao_horizon(p_environment);
	settings.sharpness = environment_get_ssao_sharpness(p_environment);
	settings.full_screen_size = p_render_buffers->get_internal_size();
	ss_effects->ssao_allocate_buffers(p_render_buffers, rb_data->ss_effects_data.ssao, settings);
	for (uint32_t v = 0; v < p_render_buffers->get_view_count(); v++) {
		ss_effects->generate_ssao(p_render_buffers, rb_data->ss_effects_data.ssao, v, p_normal_buffers[v], p_projections[v], settings);
	}
}
void RenderForwardClustered::_process_ssil(Ref<RenderSceneBuffersRD> p_render_buffers, RID p_environment, const RID *p_normal_buffers, const Projection *p_projections, const Transform3D &p_transform) {