Score the run on a triple play?

[teebob21]

So...this is brought to you all by Third World Sports(TM)...aka middle school softball. This happened to me tonight. Single man umpiring, but that's not relevant to the play. NFHS rules, with modifications for a pitching machine (again, not relevant to the play).

Bases loaded, no outs. For convention's sake, R1 on 1B, R2 on 2B, R3 on 3B. The pitch is lined to F6 for a catch (Out #1). All runners leave on contact. F6 throws to F5, who never touches 3B, but F5 does tag R2 off the base for Out #2. The ball is then overthrown to 2B where F9 picks it up and throws to the pitcher, who misplays it. F2 gets the ball and throws again to to F4 at 2B where R1 is standing in contact with the base. She makes the tag, and says "She never tagged up!" This is a valid live-ball appeal, for Out #3.

Everyone leaves the field on the L6-5-9-1-2-4 triple play.

Here's what I realized later: R3 scored on a time play. No one picked up on it at the time, including me! I know she could have been ruled out for leaving before the ball was touched for a fourth-out appeal, but that never happened.

Question: What is the proper time-play mechanic here? Do we point to the plate and alert the scorekeeper like usual on a time play? If so, does this unfairly alert the defense to an appeal opportunity?