How to add an attribute to CkEditor 4.x iframe tag
As a quick and dirty work-around, I used jquery to add a parameter to the url (which always has at least one parameter already, thus the ampersand).

$('iframe').each(function() {
      $(this).attr("src", $(this).attr("src") + '&amp;wmode=transparent')
  });

But I want to later refine this to only target urls starting with https://www.youtube.com at the very least and use an attribute instead of a parameter. If anyone can suggest the code for that based on what's above, that would be appreciated. If not, I'll eventually update this post with that code when I have more time to figure it out. Thanks.