### 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)

first_aabb = true;
	_update_scene();
	base_viewport->add_child(scene);
	inspector->edit(nullptr);
	if (first_aabb) {
		contents_aabb = AABB(Vector3(-1, -1, -1), Vector3(2, 2, 2));
		first_aabb = false;
	}
	popup_centered_ratio();
	_update_view_gizmos();
	_update_camera();
	
	scene_tree->get_root()->select(0);
	if (p_for_animation) {
		set_title(vformat(TTR("Advanced Import Settings for AnimationLibrary '%s'"), base_path.get_file()));
	} else {
		set_title(vformat(TTR("Advanced Import Settings for Scene '%s'"), base_path.get_file()));
	}
}
SceneImportSettings *SceneImportSettings::singleton = nullptr;
SceneImportSettings *SceneImportSettings::get_singleton() {
	return singleton;
}
Node *SceneImportSettings::get_selected_node() {
	if (selected_id == "") {
		return nullptr;
	}
	return node_map[selected_id].node;
}
void SceneImportSettings::_select(Tree *p_from, String p_type, String p_id) {