That’s a separate instance for the panel.
EditDomain -c dns,provider=cloudflare cyberhorse.com.au
When a default value is changed, we don’t want to potentially catastrophically undo all per-account changes. Imagine what would happen if you ran cpcmd scope:set dns.default-provider null and it deleted every DNS zone across every account 
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As for Apache handling traffic on all accounts - what does httpd -k restart report, same errors verbatim? If so, PM me the contents from /etc/httpd/conf/httpd-custom.conf and /etc/httpd/conf/virtual-httpd-built (or /etc/httpd/conf/virtual-httpd-built.bad if it exists).