### 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)

r_lightmap_caches.insert(i, lightmap_cache);
									break;
								}
								if (new_md5 == md5) {
									break;
								}
							}
						}
					}
				}
				if (generate_lods) {
					Array skin_pose_transform_array = _get_skinned_pose_transforms(src_mesh_node);
					src_mesh_node->get_mesh()->generate_lods(merge_angle, split_angle, skin_pose_transform_array);
				}
				if (create_shadow_meshes) {
					src_mesh_node->get_mesh()->create_shadow_mesh();
				}
				if (!save_to_file.is_empty()) {
					Ref<Mesh> existing = ResourceCache::get_ref(save_to_file);
					if (existing.is_valid()) {
						
						existing->reset_state();
					}
					mesh = src_mesh_node->get_mesh()->get_mesh(existing);
					ResourceSaver::save(mesh, save_to_file); 
					mesh->set_path(save_to_file, true); 
				} else {
					mesh = src_mesh_node->get_mesh()->get_mesh();
				}
			} else {