Since DNS already have some id fields, here's how they can potentially implement it:
When the user sign up and add devices, have them visit a unique subdomain to "activate" the device. On the load balancer level the device should be fingerprinted and stored, I think their VPN product already does this so it should be quite straightforward. Every DNS query can now be matched against a custom block list. Of course this would take more server resources. Cloudflare can turn this into a business opportunity by offering tiered plans, with higher level plans so that users can choose what to censor based on their own brand of politics, instead of a third party corporation. Or perhaps they can simply recover the additional server costs through selling analytics.