How do I dynamically change an autocomplete route for a field depending on another field's value?
If I understand your question correctly, you may want to include one term reference field for each taxonomy you want included on the form. You could then create a template for the page and use Javascript to control which fields are visible. So if the user chooses Option A  it gives them one set of choices for the Taxonomy and if they choose B it gives them another.. 

You may also have luck with https://www.drupal.org/project/conditional_fields