### 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)

for (int i = 0; i < post_importer_plugins.size(); i++) {
			post_importer_plugins.write[i]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE, p_root, p_node, Ref<Resource>(), node_settings);
		}
		if (post_importer_plugins.size()) {
			List<StringName> anims;
			ap->get_animation_list(&anims);
			for (const StringName &name : anims) {
				if (p_animation_data.has(name)) {
					Ref<Animation> anim = ap->get_animation(name);
					Dictionary anim_settings = p_animation_data[name];
					{
						
						List<ImportOption> iopts;
						get_internal_import_options(INTERNAL_IMPORT_CATEGORY_ANIMATION, &iopts);
						for (const ImportOption &F : iopts) {
							if (!anim_settings.has(F.option.name)) {
								anim_settings[F.option.name] = F.default_value;
							}
						}
					}
					for (int i = 0; i < post_importer_plugins.size(); i++) {
						post_importer_plugins.write[i]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_ANIMATION, p_root, p_node, anim, anim_settings);
					}
				}
			}
		}
	}
	return p_node;
}
Ref<Animation> ResourceImporterScene::_save_animation_to_file(Ref<Animation> anim, bool p_save_to_file, String p_save_to_path, bool p_keep_custom_tracks) {