If you look way back through the forums the nav beacons were actually there for us to jump into rather than at the star (where possible). Something I wholly expect to come back once players of beta complain about that extra button press to drop in at the nav beacon...
It would also make sense for a little inter system star "hop" using these if such a thing really have to be added. Means pirates can still have a decent crack at them (& me).
Yes, you're right, way way back in premium beta this is what they were for but the idea was discarded because it sucked
When I said "originally" I meant from launch, sorry. Their actual origin was indeed as you say, but FD were never going to revert back to that (again because it sucked) so, for a couple years, they remained placeholder spawn locations with no valid reason. Until this was introduced, which I think was the best solution.
Also, sadly, Sandro has gone on record to say they've no intention to introduce mini hops intra system.