It’s not useless, it removes a lot of the tracking cookies and such and sponsored links loaded with telemetry. Theoretically you can also get the benefits of anonymity if you proxy through Tor or a VPN, which I originally tried to do but turns out Google at least blocks requests from Tor and at least the VPN endpoint I have and probably most of them. Google or whatever upstream SE can still track you by IP when you self host, but its tracking is going to much less without the extra telemetry cookies and tracking code it gets when you use Google results directly.
But yes, practically you either have to trust the instance you’re using to some extent or give up some of the anonymity. I opted to self host and would recommend the same over using a public instance if you can, personally. And if privacy is your biggest concern, only use upstream search providers that are (or rather, claim to be) more privacy respecting like DDG or Qwant. My main use case is primarily as a better frontend to search without junk sponsored results and privacy is more of a secondary benefit.
FWIW, they have a pretty detailed discussion on why they recommend self-hosting here.
The message you’re reading applies to the checkbox above for encryption, not the preferences url. The preferences key only needs to be set if you want to encrypt the configuration URL, it doesn’t affect what OP wants to do.
My memory is a bit fuzzy because I switched to Searxng after playing with Whoogle briefly, but I thought Whoogle stored preferences in a cookie or something similar; the preferences URL is for when you want to transfer the preferences for your current machine to another. So OP is misunderstanding what it’s for.
OP: if your preferences aren’t sticking, are you maybe blocking cookies entirely or something? I’m pretty sure you shouldn’t need to do anything with the preferences URL for your preferences to stick if everything is set up correctly, it’s only for transferring your preferences to another machine.