There is a solution for that -- install a local resolver that makes queries using DoT/DoH/DNSCurve/DNS-over-WireGuard/whatever but answers them using ordinary UDP DNS, then make that your DNS server in /etc/resolv.conf.
The default configuration for most linux distros is to set 127.0.0.1 as the resolver in /etc/resolv.conf, and then something like systemd-resolved takes care of doing the "right thing".