🇩🇰Denmark @FrittenKeeZ

@ExTexan I managed to get it working by manually rendering the twig files and parse the markup along to body within hook_mail.

$module_path = \Drupal::service('extension.list.module')->getPath('my_module');
$template = $module_path . '/templates/email-body--' . str_replace('_', '-', $key) . '.html.twig';
$markup = twig_render_template($template, ['message' => compact('params'), 'theme_hook_original' => 'email_body']);
$message['body'] = [$markup];
$message['format'] = 'text/html';

Then I added the wrapper template file which sole content is {{ body | raw }}

/**
 * Implements hook_theme().
 */
function my_module_theme($existing, $type, $theme, $path) {
  // Copied from email-wrap theme hook.
  return [
    'email_wrap__my_module' => [
      'template' => 'email-wrap--my-module',
      'variables' => [
        'email' => NULL,
        'body' => '',
        'is_html' => TRUE,
      ],
    ],
  ];
}

Marking as fixed, because that's the limit of how much of my time I wish to give you for free😃.

Seeing as the documentation is clearly lacking, both in terms of migrating from Swiftmailer and how to use Twig and custom params with the new EmailBuilder, I can't possible think of a reason why you would mark this as fixed - you might as well just close this issue as you don't seem interested in getting that functionality to work.