A stuffing box is used to keep a majority of water coming through where the shaft enters the vessel below the water line. To your point they would still need a type of caulking between all the seams.
BTW have you ever changed shaft packing while the boat was in the water? I dont recommend doing this unless you really know what youre doing. It can lead to some anxious moments. :)
The reason I said that is because it is my understanding that the standard packing used in the typical stuffing box needs the water it keeps out to keep itself lubricated and swollen. I’ve seen old dried out packing, it’s usually in pieces.
I guess what you are describing above the water line uses another type of packing? and it’s called a stuffing box? Who knew ;) I’m too literal, ugh.
And no, I have never had the pleasure of attempting that chore in the water. I race OPB’s (Other Peoples Boats)