### 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)

item->set_text(1, path);
						if (FileAccess::exists(path)) {
							item->set_text(2, "Warning: File exists");
							item->set_tooltip_text(2, TTR("Existing file with the same name will be replaced."));
							item->set_icon(2, get_theme_icon(SNAME("StatusWarning"), SNAME("EditorIcons")));
						} else {
							item->set_text(2, "Will create new File");
							item->set_icon(2, get_theme_icon(SNAME("StatusSuccess"), SNAME("EditorIcons")));
						}
						item->add_button(1, get_theme_icon(SNAME("Folder"), SNAME("EditorIcons")));
					}
				} else {
					item->set_text(2, "No import ID");
					item->set_tooltip_text(2, TTR("Material has no name nor any other way to identify on re-import.\nPlease name it or ensure it is exported with an unique ID."));
					item->set_icon(2, get_theme_icon(SNAME("StatusError"), SNAME("EditorIcons")));
				}
				save_path_items.push_back(item);
			}
			external_paths->set_title(TTR("Extract Materials to Resource Files"));
			external_paths->set_ok_button_text(TTR("Extract"));
		} break;
		case ACTION_CHOOSE_MESH_SAVE_PATHS: {
			for (const KeyValue<String, MeshData> &E : mesh_map) {
				MeshData &md = mesh_map[E.key];
				TreeItem *item = external_path_tree->create_item(root);
				String name = md.mesh_node->get_text(0);
				item->set_cell_mode(0, TreeItem::CELL_MODE_CHECK);
				item->set_icon(0, get_theme_icon(SNAME("Mesh"), SNAME("EditorIcons")));
				item->set_text(0, name);
				if (md.has_import_id) {