Happened again at the day of this posting, AutoSSL times out, the internal cPanel error with the certificates was:
The installed certificate does not cover this domain
All of a sudden, three hours later, the certificates are fine. No word from the providers as yet, so just in case they missed it, requested a reason for the outage. The certificates are to expire in two weeks time, wonder if this is some kind of “nudge” to make preparations for their renewal, or just another bog standard glitchy software stall.