### 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)

mi->set_name(fixed_name);
						}
					}
				} else {
					memdelete(p_node);
					p_node = nullptr;
				}
			}
		}
	} else if (_teststr(name, "vehicle")) {
		if (isroot) {
			return p_node;
		}
		Node *owner = p_node->get_owner();
		Node3D *s = Object::cast_to<Node3D>(p_node);
		VehicleBody3D *bv = memnew(VehicleBody3D);
		String n = _fixstr(p_node->get_name(), "vehicle");
		bv->set_name(n);
		p_node->replace_by(bv);
		p_node->set_name(n);
		bv->add_child(p_node);
		bv->set_owner(owner);
		p_node->set_owner(owner);
		bv->set_transform(s->get_transform());
		s->set_transform(Transform3D());
		p_node = bv;
	} else if (_teststr(name, "wheel")) {
		if (isroot) {
			return p_node;
		}