### 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)

switch (p_what) {
		case NOTIFICATION_READY: {
			connect("confirmed", callable_mp(this, &SceneImportSettings::_re_import));
		} break;
		case EditorSettings::NOTIFICATION_EDITOR_SETTINGS_CHANGED: {
			inspector->set_property_name_style(EditorPropertyNameProcessor::get_settings_style());
		} break;
	}
}
void SceneImportSettings::_menu_callback(int p_id) {
	switch (p_id) {
		case ACTION_EXTRACT_MATERIALS: {
			save_path->set_title(TTR("Select folder to extract material resources"));
			external_extension_type->select(0);
		} break;
		case ACTION_CHOOSE_MESH_SAVE_PATHS: {
			save_path->set_title(TTR("Select folder where mesh resources will save on import"));
			external_extension_type->select(1);
		} break;
		case ACTION_CHOOSE_ANIMATION_SAVE_PATHS: {
			save_path->set_title(TTR("Select folder where animations will save on import"));
			external_extension_type->select(1);
		} break;
	}
	save_path->set_current_dir(base_path.get_base_dir());
	current_action = p_id;
	save_path->popup_centered_ratio();
}
void SceneImportSettings::_save_path_changed(const String &p_path) {