How do I override a RenderElement?
Using hook_element_info_alter() would be one option, not sure it's the best. 

The existing class sets 2 pre render callbacks, which you can override in your own class:

function MYMODULE_element_info_alter(array &amp;$types) {
  $types['html_tag']['#pre_render'] = [
    [\Drupal\mymodule\HtmlTag::class, 'preRenderConditionalComments'],
    [\Drupal\mymodule\HtmlTag::class, 'preRenderHtmlTag'],
  ];
}

...

namespace Drupal\mymodule;

use Drupal\Core\Render\Element\HtmlTag as CoreHtmlTag;

class HtmlTag extends CoreHtmlTag {

  public function preRenderHtmlTag($element) {
    // ...
  }

  public function preRenderConditionalComments($element) {
    // ...
  }

}