I'm using cloudflared [0] for this. Allows me to have system level DoH and everything uses it (unless explicitly configured not to). Working on Linux machines (amd64 and aarch64) and MacOS.
The documentation is not great / accurate but with a bit of fiddling I have it running as a systemd service (launchctl on MacOS). I'm using the /metrics endpoint to get details in Prometheus on the stats.
0. https://github.com/cloudflare/cloudflared
