### 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)

external_path_tree->set_column_custom_minimum_width(1, 100 * EDSCALE);
	external_path_tree->set_column_title(1, TTR("Path"));
	external_path_tree->set_column_expand(2, false);
	external_path_tree->set_column_custom_minimum_width(2, 200 * EDSCALE);
	external_path_tree->set_column_title(2, TTR("Status"));
	save_path = memnew(EditorFileDialog);
	save_path->set_file_mode(EditorFileDialog::FILE_MODE_OPEN_DIR);
	HBoxContainer *extension_hb = memnew(HBoxContainer);
	save_path->get_vbox()->add_child(extension_hb);
	extension_hb->add_spacer();
	extension_hb->add_child(memnew(Label(TTR("Save Extension:"))));
	external_extension_type = memnew(OptionButton);
	extension_hb->add_child(external_extension_type);
	external_extension_type->add_item(TTR("Text: *.tres"));
	external_extension_type->add_item(TTR("Binary: *.res"));
	external_path_tree->set_hide_root(true);
	add_child(save_path);
	item_save_path = memnew(EditorFileDialog);
	item_save_path->set_file_mode(EditorFileDialog::FILE_MODE_SAVE_FILE);
	item_save_path->add_filter("*.tres", TTR("Text Resource"));
	item_save_path->add_filter("*.res", TTR("Binary Resource"));
	add_child(item_save_path);
	item_save_path->connect("file_selected", callable_mp(this, &SceneImportSettings::_save_path_changed));
	save_path->connect("dir_selected", callable_mp(this, &SceneImportSettings::_save_dir_callback));
	update_view_timer = memnew(Timer);
	update_view_timer->set_wait_time(0.2);
	update_view_timer->connect("timeout", callable_mp(this, &SceneImportSettings::_update_view_gizmos));
	add_child(update_view_timer);
}
SceneImportSettings::~SceneImportSettings() {