### 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 (!animation_map.has(p_name)) {
		AnimationData ad;
		ad.animation = p_anim;
		_load_default_subresource_settings(ad.settings, "animations", p_name, ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_ANIMATION);
		animation_map[p_name] = ad;
	}
	AnimationData &animation_data = animation_map[p_name];
	Ref<Texture2D> icon = get_theme_icon(SNAME("Animation"), SNAME("EditorIcons"));
	TreeItem *item = p_tree->create_item(p_parent);
	item->set_text(0, p_name);
	item->set_icon(0, icon);
	item->set_meta("type", "Animation");
	item->set_meta("import_id", p_name);
	item->set_selectable(0, true);
	animation_data.scene_node = item;
}
void SceneImportSettings::_fill_scene(Node *p_node, TreeItem *p_parent_item) {