The DNS tool cpdig seems not to be working correctly. I've turned off ipv6 on the server, and it still keeps trying to use ipv6 for DNS queries. Is ipv6 required to use cPanel/WHM and autossl?
cPanel's AutoSSL doesn't require IPv6 to function. However, cpdig by default verify over IPv6 and IPv4. When troubleshooting why a DNS record isn't returning, it is generally best to make sure the DNS is fully working the way cPanel expects.
The cpdig tool uses LibUnbound to verify DNS records. The LibUnbound performs DNS lookups at the root nameservers and recursively makes it down to the domain's DNS "A" record.
The below articles will be of use for further investigating AutoSSL resolution problems.