Now question creation become more complicated, but there are no reason to use extra_question_fields() in get_question_options and not use it in initialise_question_instance. Otherwise it prevents extra_question_fields() from functioning properly.

Shortanswer question should rely on extra_question_fields() instead of hardcoding $usecase there.

That's actually quite easy, so please do. Preg question type class still inherited from shortanswer, and it has quite more extra question fields.