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Doesn't the RPi still go through the ISP? You'd still have to find a way to bypass their hijacking attempts, just on a different device this time.
You'd have to use DNS over HTTPS, DNS over TLS, or DNS over QUIC. As far as I know, PiHole doesn't support these out-of-the-box, so AdGuard Home is a better choice (it's like PiHole but more powerful).
I know PiHole had plans to implement this though, so maybe they do support it now.
You can do it. I set mine up ages ago. https://docs.pi-hole.net/guides/dns/cloudflared/
It's not out-of-the-box though, and requires a bunch of manual setup. On AdGuard Home you just need to enter the DNS URL into the UI and that's it.