It would make more sense if was just : "Feel free to do as you please".
The question would be : Is he in the kitchen?
No. Cogitate is both transitive and intransitive, that is we may cogitate something and cogitate about something. But we do not cogitate that... in the sense of forming an opinion about it.
Call it a day means to stop doing something, finish. That's enough, let's call it a day and go home.