Am I missing something? I have "Keep window open when it loses focus" unchecked but Yakuake will not autohide. I tried checking that option - nope. Unchecking afterward... nope. The only way I can dismiss it is to rehit the hotkey, F12 in my case. Thanks.
What branch are you on? It works okay for me on testing
Sometimes it helps to close Yakuake and then restart it in order for certain changes to its configuration to take effect. Have you tried this?