I think there's some confusion here. The usual callsign labels are derived from flightplan info linked to the transponder setting given to the aircraft. However, I believe that Mode S "callsigns" are set by the crew. Otherwise why would many of them be in error, or contain nonsense and even "rude" words? Plus, a significant proportion of aircraft do not transmit callsigns. Until about 12 months ago transmitted callsigns were unreliable but they have improved of late, possibly as a result of publicity to crews?
I'm currently looking at Mode S info from 50+ aircraft in the London area, of which around 15 are not transmitting callsigns.