Two advantages of a separate box:-
(1) As Prime Time alluded to, with a separate box you will usually get two tuners (Freesat+ as opposed to Freesat alone), meaning you can record one channel whilst watching another, or record two channels simultaneously;
(2) With a seperate box, if you wanted to archive to an external recorder, i.e. a DVD recorder, you would not need to have the TV switched on to do this. If your only Freesat tuner was in the TV, then not only would the TV need to be switched on if you wanted to record from its tuner, but you might also have to have the TV showing the output from its satellite tuner, rather than watching something else on Freeview, or on DVD or Blu Ray or cable, or playing a game on it using a connected console.
The main disadvantage of having the tuner in a seperate box rather than built into the TV is the extra room taken up by the seperate box and the extra cables needed to connect the Freesat box to the TV and the power socket.