Just to stir the pot a little I want to add one more complication to the situation. This came up at my preseason clinic and then again at one of my association meetings and basically we ended up with a bunch of respected veterans arguing about what they would do. About half said they would follow the approved interpretation (signal safe and then wait for an appeal) and the other half saying that the approved interp was garbage and would lead to more problems than it solves. (And thus they would make no call at first and wait; if the runner "retouched" first base before F3 tagged the runner or touched the base while in possession of the ball they would rule him safe, otherwise they would rule him out.)
Now the fun part.
1) What if the BR beats the throw to first by a step (but misses first) and F3 catches the ball still in contact with the bag. (Approved ruling says he is safe, and signaled as such, and and since there can be no inadvertant appeals, then a proper appeal must still occur for an out to be recorded.) BUT, what if the BR immediately realizes his mistake and very quickly returns to first. The defensive coach immediately yells at his fielder to tag the runner, but the tag occurs after the BR has retouched the base. A) F3 is in contact with the base from the time he catches the ball until the time he makes the tag, or B)F3 leaves the base after receiving the ball but before attempting the tag of the BR.
2) What if the ball becomes dead? Situation: 2 Outs, R3, R2 ground ball to F5 who looks R3 back to third and then throws late to F3, but after receiving the ball (while in contact with 1st base after the BR has passed, but not touched first), F3 throws home to attempt to retire R3. R3 is safe, but F2 then throws to F5 and retires R2 to end the inning (and making the ball dead). Now a successful appeal would negate the run. What if the defensive coach verbally appeals with the runner standing on: A) first base, B) the first base line 15 ft beyond 1st base, C) on 2nd base after retouching first, or D) on second after failing to ever re-touch first, E) half a step from first and running as hard as he can towards first in an attempt to retouch.
3) What if F2 had seen that he couldn't get R3 out, but HAD seen the BR miss first. As the BR tried to return to first F2 intentionally throws the ball out of play and starts yelling, "He missed first, I'm appealing that the Batter-Runner missed first!" (a far-fetched, but legal dead ball appeal).
All thoughts appreciated.