### 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)

} else {
						item->set_text(2, "Will save to new File");
						item->set_icon(2, get_theme_icon(SNAME("StatusSuccess"), SNAME("EditorIcons")));
					}
					item->add_button(1, get_theme_icon(SNAME("Folder"), SNAME("EditorIcons")));
				}
				save_path_items.push_back(item);
			}
			external_paths->set_title(TTR("Set paths to save animations as resource files on Reimport"));
			external_paths->set_ok_button_text(TTR("Set Paths"));
		} break;
	}
	external_paths->popup_centered_ratio();
}
void SceneImportSettings::_save_dir_confirm() {
	for (int i = 0; i < save_path_items.size(); i++) {
		TreeItem *item = save_path_items[i];
		if (!item->is_checked(0)) {
			continue; 
		}
		String path = item->get_text(1);
		if (!path.is_resource_file()) {
			continue;
		}
		String id = item->get_metadata(0);
		switch (current_action) {
			case ACTION_EXTRACT_MATERIALS: {
				ERR_CONTINUE(!material_map.has(id));
				MaterialData &md = material_map[id];
				Error err = ResourceSaver::save(md.material, path);