I know about the Nav beacon, no confusion there. I'm concerned with the FSS after honking. All FSS signals are already discovered, as if I had already completed the FSS mini-game. That happens before I even target the beacon.
Well in a system which you don't have the data for, all the FSS does when you honk is tell you how many bodies there are, opening the FSS screen tells you how many signals are in the system. The only things the FSS "discovers" without doing the tuning and zooming are stellar bodies and things within the passive detection range (30ls). In those systems which your Nav has the data for
* (albeit the system appears "unknown" until you arrive) - you don't need to FSS to get the bodies' details and composition but (I think) you need to FSS them to see if there are bio or geo features - that last bit might be wrong.
* i.e. those over a certain population (2million?)
Maybe I am not understanding your issue, sorry.