Do you mean when communicating directly with a root DNS server over unencrypted UDP or TCP? You're right. There's currently no universal way to encrypt direct queries to root DNS servers. To work around this, the best approach is to host your own public DNS server outside your untrusted ISPs network and connect to it securely using DoH, DoQ, or DoT. Alternatively, you can rely on a trusted third-party public DNS provider that supports encrypted connections. In the end, there's no perfect solution. You have to choose who to trust. Personally, I trust my ISP more than external DNS providers. For anonymity you could route your DNS root queries throe tor or a VPN for the cost of performance.

I also used third-party public resolvers before. Mainly FFM (its not on the list) but non-profit, EU and encrypted. If you boil down the list (from the website) to this categories, you have 4 providers. You can trust, in my opinion. But the problem with all this provider is, that you ran quick into rate limits or some query type restrictions. Especially if you run your own mail server or other DNS expensive task.

Fun fact about hosting your own DNS infrastructure and offering it to friends and family: They might actually trust other providers more than they trust you. Even if they know and trust you personally. Because they know you can theoretically read their queries, it’s more convenient for them to have a stranger do it instead.