I don't see any option that would be natural in such a sentence and would denote the difference between "over there" and "there". In other contexts an a bit colloquial construction "o tam" could work. With pointing the direction with your finger.
"Kto tam?" is the obvious, natural way of saying "Who's there?" when someone is knocking on your door, but I think that if the English sentence had "over there", it's not a good translation. As it generally only works when someone is knocking.
So what is exactly the difference between "Kto jest tam?" and "Kto tam jest?" ? Personally I would have chosen "Kto jest tam?" - as the questions are usually structered like that in the past lessons above.
But would you say "Who is over there?" if someone knocked on the door? Because we added that "over" exactly to discourage people from thinking about the 'knock on the door' situation, for which "Kto tam jest?" would be at least unusual.