Can I specify the DNS resolver to be used for DNS challenge with certbot similar to traefik?

Certbot doesn't do any DNS resolving of your domains. Error states that Let's Encrypt's own resolvers cannot resolve your DNS record. As for why that happens: could be that your authoritative servers are not fully synced (LE resolver only ever try resolving ONCE using a random authoritative server of the domain that requires authorization) or something else.

But since you didn't share your domain name—help from this forum will be limited.