I'll take a shot here at number 2. U1's statement that the runner had broken before the pitcher had started his move is HIS judgment. U3, in calling the balk as throwing to an unoccupied base, presumably knows the rule and HIS judgment was that the runner had not left before the move started (that's why he made the call). So it can't be overturned, via Appendix E. It's only a gross misapplication of the rules if U1's judgment of the play is accepted as fact and U3 did not take that into account in his call because he was looking at his counter...which NCAA guys by definition don't do
Yes, apparent contradiction in case one, but it looks like they want 8-5e to take precedence due to the double play. 8-5e:
"If the batter-runner interferes intentionally or unintentionally with a
batted ball or the fielder fielding it, with a double play likely, the batter-
runner and the runner closest to home plate are out, regardless of where
the double-play attempt may have taken place; "