### 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 (mesh.is_valid()) {
				p_dictionary.importer_meshes.insert(mesh);
			}
			Ref<Skin> skin = mesh_instance_3d->get_skin();
			if (skin.is_valid()) {
				p_dictionary.skins.insert(skin);
			}
		}
	}
	AnimationPlayer *animation_player = Object::cast_to<AnimationPlayer>(p_node);
	if (animation_player) {
		List<StringName> animation_list;
		animation_player->get_animation_list(&animation_list);
		for (const StringName &E : animation_list) {
			Ref<Animation> animation = animation_player->get_animation(E);
			p_dictionary.animations.insert(animation);
		}
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		Node *child = p_node->get_child(i);
		_populate_scalable_nodes_collection(child, p_dictionary);
	}
}
void _apply_permanent_rotation_scale_to_node(Node *p_node) {
	Transform3D transform = Object::cast_to<Node3D>(p_node)->get_transform();
	ScalableNodeCollection scalable_node_collection;
	_populate_scalable_nodes_collection(p_node, scalable_node_collection);
	_apply_basis_to_scalable_node_collection(scalable_node_collection, transform.basis.get_scale());
}
Node *ResourceImporterScene::_pre_fix_node(Node *p_node, Node *p_root, HashMap<Ref<ImporterMesh>, Vector<Ref<Shape3D>>> &r_collision_map, Pair<PackedVector3Array, PackedInt32Array> *r_occluder_arrays, List<Pair<NodePath, Node *>> &r_node_renames) {