For PiHole today, most everything comes over port 53, and thus easy to track, monitor and block as required.

Tomorrow, DNS requests can be on any port, to any server, on any protocol. This makes trying to use a single point of control like the PiHole so much harder than it was in the past. Who is to say next week its HTTPS as the encrypted transport for DNS? Use whatever bizarre encryption scheme you like. It's your app... The app can just ignore whatever DNS server you suggested via DHCP or whatever and go back to its homebrew domain name resolution system.