If the 1st baseman had been on the foul side of first, the throw probably should have been easier for the ump to call?
If the pitcher had hit the runner in the back, the call should have been "OUT" for a running lane violation. As it happened, the batter/runner was not hit and the pitcher had to throw over top of the runner. Result: safe!
As far as the batter being hit in the knee with the ball, just one of those things NO ONE saw!
The best team won that night & that series.