Well, a reasonable reply, but unsatisfactory indeed. IMO webserver is one major part of the server, and recently it allows almost zere config options. Suggestions were put into database, and even accepted. It would be enough to have one big field, to edit custom settings.
No problem for me going to console, and add my directive to the apache config, but in such a case, without such custom configs being included into the config-backup, it just makes claims like "easy ability to recover your server" not entirely correct. What is server config recovery good for, if all my domains are left in the water? You know the name of the directory, where those configs are being put, so you could easily include it into the backup.
Imo config recovery should be complete, if possible, so that the "only" thing admin needs to do, is to - upload data, and be done :-)