### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

back_buffer_rect = Rect2();
						backbuffer_gen_mipmaps = md->shader_data->uses_screen_texture_mipmaps;
					} else if (!material_screen_texture_mipmaps_cached) {
						backbuffer_gen_mipmaps = md->shader_data->uses_screen_texture_mipmaps;
					}
				}
				if (md->shader_data->uses_sdf) {
					r_sdf_used = true;
				}
				if (md->shader_data->uses_time) {
					time_used = true;
				}
			}
		}
		if (ci->skeleton.is_valid()) {
			const Item::Command *c = ci->commands;
			while (c) {
				if (c->type == Item::Command::TYPE_MESH) {
					const Item::CommandMesh *cm = static_cast<const Item::CommandMesh *>(c);
					if (cm->mesh_instance.is_valid()) {
						mesh_storage->mesh_instance_check_for_update(cm->mesh_instance);
						mesh_storage->mesh_instance_set_canvas_item_transform(cm->mesh_instance, canvas_transform_inverse * ci->final_transform);
						update_skeletons = true;
					}
				}
				c = c->next;
			}
		}
		if (ci->canvas_group_owner != nullptr) {
			if (canvas_group_owner == nullptr) {