For calculation take off performance, do they use the expected fuel mass they put initially or the real fuel?
They should use the actual take off mass = actual zero fuel weight + Total fuel on board.
The confusion seems to be due to the artificial increase of zero fuel weight by 700 kgs.
The trapped unusable fuel in the centre tank simply reduces the
maximum zero fuel weight by the same amount. i.e. you can't carry as much baggage / passengers as you might want.
The actual zero fuel weight and actual fuel on board should be entered as usual. The useable fuel for range / endurance calculations = Actual fuel on board - any unusable fuel.