Why and how does $node->taxonomy change in hook_nodeapi?

I'm connecting terms to a node in some different situations and I'm a bit confused by how $node->taxonomy behaves differently in different situations.

I have an xml import sort of like this:

  // Checks if the node exists
  if ($nid) {
    $node = node_load($nid, NULL, TRUE);
  } 
  else {
    $node = new stdClass();
    $node->type        = 'type';
    $node->uid         = 1;
    $node->title       = '';
    $node->model       = $model;
    $node->sell_price  = 0;
    # etc..
  }
  
  // Adds the term
  $tid = trim($product->getElementsByTagName('tid')->item(0)->nodeValue;
  $node->taxonomy[$tid] = $tid;

  // Saves the node
  node_save($node);

Obviously the above is simplified, but that's the important bits. It works perfectly. Note how I'm adding the terms here.

And i also have something like this:

function mymodule_nodeapi(&$node, $op, $a3 = NULL, $a4 = NULL) {
  switch ($op) {
    case 'presave':
      // Empties taxonomy[$vid] to avoid duplicate terms
      $node->taxonomy[$vid] = array();
      // Connects the node to a term depending on the value in field_fmt
      switch ($node->field_fmt[0]['value']) {
        case 1:
          $node->taxonomy[$vid][$tid1] = $tid1;
          break;
        case 2:
          $node->taxonomy[$vid][$tid2] = $tid2;
          break;
        default:
          $node->taxonomy[$vid][$tid3] = $tid3;             
      }  
      break;
  }
}

Here I have to add the terms differently.

How and when did the structure of $node->taxonomy change when 'presave' is called on the very first line of the node_save() function?

function node_save(&$node) {
  // Let modules modify the node before it is saved to the database.
  node_invoke_nodeapi($node, 'presave');

I don't understand why I suddenly need to specify the vocabulary ID in 'presave' when I didn't before node_save. Also, I understand that the syntax is different in 'presave' depending on whether the vocabulary is tags, single select or multi select. Why isn't it just $node->taxonomy[$tid] = $tid always?

Also, are there better ways of connecting terms to nodes?

Thanks in advance and apologies if this has been asked before. I've googled the topic a lot, but everyone seems to have different opinions on how to connect terms to nodes programmatically.