Obstruction by definition, is "The act of a defensive team member who B) impedes the progress of the runner or batter-runner who is legally running the bases unless the fielder is:
1. in possession of the ball
2. in the act of fielding a batted ball. NOTE: Contact is not necessary to impede the progress of the batter-runner or a runner.
So in the case of the shortstop, if he's not in possession of the ball or in the act of fielding a batted ball, then yes he is obstructing and the runner is protected to 3B.
The whole "he barely bumped him or wouldn't have made it any way" arguments don't work. The fielder is in the way not doing what he is supposed to be doing, fielding the ball. If he impedes the runner, his team will be penalized. Now if it's a ground ball to SS, and the fielder is charging the ball, it is the runners job to avoid that fielder so he doesn't interfere because if he does, his team will be penalized.
As for 1B on the play bobbled at 3B, it's not usually the 1B in the way on the bag waiting for a throw, because the runner would have to turn 90 degrees and should be going to the orange bag. It's usually they start running to the bag to cover, see the 3B bobble the ball and stop and watch the play in the way. Same thing with the base hit to LF where he's in the way of the runner rounding. He's probably stopped in the way. If the runner rounded 1st and took a couple of steps toward 2nd base when he ran into the 1B, the 1B obviously didn't have a play on at 1st, why is he still in the way?