That domain is shared by many people. The 1000 in the error message indicates how many were issued in the past week. My log search shows a total of over 140,000 but many of those are renewals which don't count for that particular rate limit.
That domain should probably be in the public suffix list but that has to be done by the registered domain owner.
They must have asked for a rate limit from Let's Encrypt because the default is 5 identical 50 new certs per week per registered domain - not 1,000.