Quick clarifying question on the rule you quoted in a little bit different scenario. We have had a couple of situations where a girl was called out on the base then went into the dugout. I think in each case it was a bang-bang play at a base. The coach came out to argue the call and on appeal another ump overturned the call putting the girl back on the base. I assume the rule doesn't apply because play is stopped during the argument? I have heard a few people yell "player should be out since she went in dugout" but I have never seen an ump do anything about it in the situation I just described.
The runner is only out if she abandons her effort to run the bases and/or goes into the dugout because she THINKS she is out. If the ump called her out, the runner didn't abandon the bases, she WAS called out.