It is not an automatic out if the runner is hit with the ball. It must be a quality throw, and the runner must have interfered with the player taking the throw at 1st bases ability to catch the throw. Prior to the running lane the runner has no different than any other runner, they do not have to avoid the throw, but they cannot intentionally interfere with it either. If the rule was an automatic out for hitting the runner with the ball out of the lane, it would just give the defense license to bean the runner killing the play and returning any other runners to the last base occupied.
Right - this is covered in the exception in the USSSA rule where the runner must have interfered with a fielder or a throw.
I actually saw this last year in a local travel baseball tournament - after fielding a bunt, the catcher intentionally threw into the back of the batter-runner when he had a clear lane to first base to throw in (and the player covering 1st was probably not getting there in time) and the umpire correctly awarded the base to the batter-runner and then ejected the catcher (and then the coach shortly after).