Any flying training system should (for the benefit of the students) emulate the rules and procedures used by the front line, as far as possible. Front line FJ formation renumbering is a no-no, so the training system needs to mirror this.
If this happens to tax the formation leader then I recommend the advice so often issued to students in the debrief: listen to the brief and pay attention!
It is a basic requirement that the leader knows the locations of his wingmen - he/she has briefed it! Low SA on the part of a formation leader would throw doubt on their ability to safely lead that type of sortie - something that reinforces the requirement to assess a potential leader's SA during the formation-lead check-ride.
In my experience the students cope quite well with sticking to their callsign wherever they sit in the formation - it is the QFIs that sometimes struggle!