hook_form_alter

Set taxonomy option by code

You'll need to create a custom module and use the hook_form_alter() function.

function example_form_alter(&$form, $form_state, $form_id) {
  $form['taxonomy'][2]['#default_value'] = array(0 => $term->tid);
}

Please note that the $form['taxonomy'][2]['#default_value'] is the vocabulary id.

Change select options within a nodereference

First you'll have to make use of hook_form_alter() function.

function example_form_alter(&$form, $form_state, $form_id) {
  $form['field_example_reference']['#pre_render'] = array('example_change_node_reference');
}

Now the node reference will look for a example_change_node_reference() function which will return an array of options.

function example_change_node_reference($element) {
      $element['nid']['nid']['#options'] = array($node->nid => $node->title);
  return $element;
 
}