I am not sure how Pihole currently whitelists individual domains, but is it possible to catch and exclude/whitelist items that are being loaded in from an external .conf file in the /etc/dnsmasq.d directory?
The items are in the following format: server=/something.com/
I am guessing that for this kind of purpose it would be down to the user to reference the whitelist and exclude the items before including them in a .conf file, but I just wanted to check on what is and isn't possible.