Hmm, I don’t know anything about Whoogle, but from other privacy-conscious search engines, I would expect it to work when you use that URL in your bookmark.

Three things I can imagine:

• Something in your hosting stack strips the URL parameters, like maybe your reverse proxy, if you use one. You might be able to see in the Whoogle or web server logs, which URLs actually reach it. Might need to set it to debug/trace logging.
• Maybe there’s a flag in the Whoogle configuration you need to enable to accept these preference URLs.
• It’s a bug in that Whoogle version.