### 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)

RendererRD::MeshStorage *mesh_storage = RendererRD::MeshStorage::get_singleton();
	RD::DrawListID draw_list = p_draw_list;
	RD::FramebufferFormatID framebuffer_format = p_framebuffer_Format;
	
	RD::get_singleton()->draw_list_bind_uniform_set(draw_list, render_base_uniform_set, SCENE_UNIFORM_SET);
	RD::get_singleton()->draw_list_bind_uniform_set(draw_list, p_params->render_pass_uniform_set, RENDER_PASS_UNIFORM_SET);
	RD::get_singleton()->draw_list_bind_uniform_set(draw_list, scene_shader.default_vec4_xform_uniform_set, TRANSFORMS_UNIFORM_SET);
	RID prev_material_uniform_set;
	RID prev_vertex_array_rd;
	RID prev_index_array_rd;
	RID prev_pipeline_rd;
	RID prev_xforms_uniform_set;
	bool shadow_pass = (p_pass_mode == PASS_MODE_SHADOW) || (p_pass_mode == PASS_MODE_SHADOW_DP);
	SceneState::PushConstant push_constant;
	if constexpr (p_pass_mode == PASS_MODE_DEPTH_MATERIAL) {
		push_constant.uv_offset = Math::make_half_float(p_params->uv_offset.y) << 16;
		push_constant.uv_offset |= Math::make_half_float(p_params->uv_offset.x);
	} else {
		push_constant.uv_offset = 0;
	}
	bool should_request_redraw = false;
	for (uint32_t i = p_from_element; i < p_to_element; i++) {
		const GeometryInstanceSurfaceDataCache *surf = p_params->elements[i];
		const RenderElementInfo &element_info = p_params->element_info[i];