### 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 (scene_state.used_depth_texture) {
		RENDER_TIMESTAMP("Copy Depth Texture");
		
		_render_buffers_copy_depth_texture(p_render_data);
	}
	RENDER_TIMESTAMP("Render 3D Transparent Pass");
	RD::get_singleton()->draw_command_begin_label("Render 3D Transparent Pass");
	rp_uniform_set = _setup_render_pass_uniform_set(RENDER_LIST_ALPHA, p_render_data, radiance_texture, true);
	_setup_environment(p_render_data, is_reflection_probe, screen_size, !is_reflection_probe, p_default_bg_color, false);
	{
		uint32_t transparent_color_pass_flags = (color_pass_flags | COLOR_PASS_FLAG_TRANSPARENT) & ~(COLOR_PASS_FLAG_SEPARATE_SPECULAR);
		RID alpha_framebuffer = rb_data.is_valid() ? rb_data->get_color_pass_fb(transparent_color_pass_flags) : color_only_framebuffer;
		RenderListParameters render_list_params(render_list[RENDER_LIST_ALPHA].elements.ptr(), render_list[RENDER_LIST_ALPHA].element_info.ptr(), render_list[RENDER_LIST_ALPHA].elements.size(), false, PASS_MODE_COLOR, transparent_color_pass_flags, rb_data.is_null(), p_render_data->directional_light_soft_shadows, rp_uniform_set, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_WIREFRAME, Vector2(), p_render_data->scene_data->lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, p_render_data->scene_data->view_count);
		_render_list_with_threads(&render_list_params, alpha_framebuffer, can_continue_color ? RD::INITIAL_ACTION_CONTINUE : RD::INITIAL_ACTION_KEEP, RD::FINAL_ACTION_READ, can_continue_depth ? RD::INITIAL_ACTION_CONTINUE : RD::INITIAL_ACTION_KEEP, RD::FINAL_ACTION_READ);
	}
	RD::get_singleton()->draw_command_end_label();
	RENDER_TIMESTAMP("Resolve");
	RD::get_singleton()->draw_command_begin_label("Resolve");
	if (rb_data.is_valid() && rb->get_msaa_3d() != RS::VIEWPORT_MSAA_DISABLED) {
		for (uint32_t v = 0; v < rb->get_view_count(); v++) {
			RD::get_singleton()->texture_resolve_multisample(rb_data->get_color_msaa(v), rb->get_internal_texture(v));
			resolve_effects->resolve_depth(rb_data->get_depth_msaa(v), rb->get_depth_texture(v), rb->get_internal_size(), texture_multisamples[rb->get_msaa_3d()]);
		}
		if (taa && rb->get_use_taa()) {
			taa->msaa_resolve(rb);
		}
	}
	RD::get_singleton()->draw_command_end_label();
	RD::get_singleton()->draw_command_begin_label("Copy framebuffer for SSIL");