True, but if you agree this works and letsencrypt becomes so popular as I guess, this might become part of drupal core.
And hopefully people will have a process to apply other .htaccess changes to a drupal core update, because it is quite normal that it can change. (.htaccess is not seen as part of the “do not ever hack core” system).
The upgrade process of drupal also mentions .htaccess as a file to give special care. (https://www.drupal.org/node/1223018)