### 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)

if (!p_save_to_file || !p_save_to_path.is_resource_file()) {
		return anim;
	}
	if (FileAccess::exists(p_save_to_path) && p_keep_custom_tracks) {
		
		Ref<Animation> old_anim = ResourceLoader::load(p_save_to_path, "Animation", ResourceFormatLoader::CACHE_MODE_IGNORE);
		if (old_anim.is_valid()) {
			for (int i = 0; i < old_anim->get_track_count(); i++) {
				if (!old_anim->track_is_imported(i)) {
					old_anim->copy_track(i, anim);
				}
			}
			anim->set_loop_mode(old_anim->get_loop_mode());
		}
	}
	if (ResourceCache::has(p_save_to_path)) {
		Ref<Animation> old_anim = ResourceCache::get_ref(p_save_to_path);
		if (old_anim.is_valid()) {
			old_anim->copy_from(anim);
			anim = old_anim;
		}
	}
	anim->set_path(p_save_to_path, true); 
	Error err = ResourceSaver::save(anim, p_save_to_path, ResourceSaver::FLAG_CHANGE_PATH);
	ERR_FAIL_COND_V_MSG(err != OK, anim, "Saving of animation failed: " + p_save_to_path);
	return anim;
}
void ResourceImporterScene::_create_slices(AnimationPlayer *ap, Ref<Animation> anim, const Array &p_slices, bool p_bake_all) {