Except, most of us access the internet with an OS. If OSs prefered encrypted DNS queries then it gives us a heap more privacy.
No, the OS has nothing to do with it. DNS is handled by a DNS client, which is run as a service. To use a particular feature you simply have to connect to a server that supports it. In the case of DNSCrypt you use a different DNS client and configure what DNSCrypt server you want to connect to within it. Then you point your normal DNS client's DNS IP to your the IP of the DNSCrypt client. https://lifehacker.com/how-to-boost-your-internet-security-with-dnscrypt-510386189