applyUpdates() is deprecated. Is it really needed in hook_install() anyway?
The change record you've linked is about update hooks for already installed modules, not hook_install().

You've never needed applyUpdates() in an install hook. If your custom module is adding a new field, it will be added automatically when the module is enabled, and removed when the module is uninstalled. There was only an issue with base fields containing data, but this is resolved since Drupal 8.5. See this change record: Base fields with existing data can now be uninstalled.