DNS updates may take up to 48-72 hours to fully propagate world wide. That may be the explanation of the error you were getting using bncert tool about your domain and DNS
problem: SERVFAIL looking up A for mydomain.com, url:
[www.mydomain.com] acme: error: 400 :: urn:ietf:params:acme
Please note the errors above are not related to the bncert tool but to lego, which is used by the bncert tool to generate the SSL certificates.
Then you got a different error using the
lego binary manually. That erorr said that port 443 was in use, that's why I suggested you to stop Apache, run the lego tool again and then start the Apache service again.
Apart from the above, I just checked the domain name present in your bnsupport bundle in the whatsmydns tool for checking DNS and it is true that some DNS servers do not have the information of your site. We recommend you to check with DNS service provider about it. You can check the DNS propagation of your domain in the link below