### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

Ref<AnimationLibrary> library;
		for (int i = 0; i < scene->get_child_count(); i++) {
			AnimationPlayer *ap = Object::cast_to<AnimationPlayer>(scene->get_child(i));
			if (ap) {
				List<StringName> libs;
				ap->get_animation_library_list(&libs);
				if (libs.size()) {
					library = ap->get_animation_library(libs.front()->get());
					break;
				}
			}
		}
		if (!library.is_valid()) {
			library.instantiate(); 
		}
		print_verbose("Saving animation to: " + p_save_path + ".scn");
		err = ResourceSaver::save(library, p_save_path + ".res"); 
		ERR_FAIL_COND_V_MSG(err != OK, err, "Cannot save animation to file '" + p_save_path + ".res'.");
	} else {
		Ref<PackedScene> packer = memnew(PackedScene);
		packer->pack(scene);
		print_verbose("Saving scene to: " + p_save_path + ".scn");
		err = ResourceSaver::save(packer, p_save_path + ".scn"); 
		ERR_FAIL_COND_V_MSG(err != OK, err, "Cannot save scene to file '" + p_save_path + ".scn'.");
	}
	memdelete(scene);
	
	
	return OK;
}