The short rivet length is to assure that after setting the shop head doesn’t protrude above the face of the spar stub ( would always be grinding into the face of the socket in the fuselage)
These rivets aren’t holding the wing on… they are only assuring that the two layers don’t separate.
BTW, if you do try and fully fill the countersink with rivet material, you will cause undue stress on the parts and they will no longer be flat (also a problem with the it to the fuselage).