It is indeed dreadful. I’ve no idea whether DTP Tools have a solution for this, you could check their website. But cross-references aren’t unproblematic: you still have to override the running-header frame to make the cross-ref catch its reference, and when text moves around and a heading moves to a different page, you end up with the wrong running header.

First, to target both opening and closing parentheses, use [()]
And set the character style in the Change Format panel.

It works fine over here. Can you show a screenshot of the Find/Change window as you you it?

Updated script to deal with empty lines in the text file.

(function () {
  var condition;
  var riskWords;
  // Remove and recreate the condition if it exists
  // so that words removed from the list are
  // 'unrisked' in the text

  function getCondition () {

    var c = app.documents[0].conditions.item('Risk word');
    
    if (c.isValid) {
      var p = c.properties;
      // This is quicker than removing the highlights in the text
      c.remove();
      c = app.documents[0].conditions.add(p);
    } else {
      app.documents[0].conditionalTextPreferences.showConditionIndicators = 
        ConditionIndicatorMode.SHOW_INDICATORS;
      c = app.documents[0].conditions.add ({
        name: 'Risk word', 
        indicatorColor: UIColors.YELLOW, 
        indicatorMethod: ConditionIndicatorMethod.useHighlight,
      });
    }
    return c;
  }

  function highlight (word) {
    app.findTextPreferences.findWhat = word;
    var w = app.documents[0].findText();
    for (var i = w.length-1; i >= 0; i--) {
      w[i].applyConditions (condition);
    }
  }

  function getWords () {
    var f = File (app.documents[0].filePath + '/risk-words.txt');
    if (f.exists) {
      f.encoding = ('utf-8');
      f.open('r');
      var w = f.read().replace(/+$/,'').split(/[\r]/);
      f.close();
      return w;
    }
    return null;
  }

  app.findTextPreferences = app.findChangeTextOptions = null;
  app.findChangeTextOptions.properties = {
    caseSensitive: false,
    wholeWord: true,
    includeLockedStoriesForFind: false,
  }

  condition = getCondition();
  riskWords = getWords();
  if (!riskWords) {
    alert ('Risk words not found');
    exit();
  }

  for (var i = riskWords.length-1; i >= 0; i--) {
    highlight (riskWords[i]);
  }

}());

I’ve seen this error a while ago, but I can’t remember what it the problem is. And I can’t reproduce it. Could you send me that document?