hawkjr,
dash_riprock gave you the correct answer, but perhaps the full implication wasn't obvious. Time was granted for a defensive conference, which means the ball was dead during the conference. The ball can't become live again, and no outs can be recorded, until.... well, just read the the rules below:
NFHS rules (but OBR and NCAA are in effect the same)
Rule 5.5
ART. 1 Ball becomes dead immediately when: ......
h. the umpire handles a live ball or calls “Time” for inspecting the ball or for any other reason, ......
ART. 2 When the ball becomes dead:
a. no action by the defense can cause a player to be put out; .......
ART. 4 After a dead ball, the ball becomes alive when it is
held by the pitcher in a legal pitching position, provided the pitcher has engaged the pitcher’s plate, the batter and the catcher are in their respective boxes, and the umpire calls “Play” and gives the appropriate signal.
You can see that the ball never becomes live "automatically". Umpires will frequently just point at the pitcher to put the ball in play, without calling "Play", but of course this isn't done until the pitcher, batter and catcher have all assumed the appropriate positions.
Furthermore, the ball simply can't become live while the third baseman is holding it. If the umpire mistakenly believes the pitcher has the ball and calls "Play", it is umpire error, and any ensuing action is voided, other than the possible ejection of the defensive manager.
As dash pointed out, it is possible for the third baseman and pitcher to get together without time being called, so that the ball is still alive. In that case, if the pitcher avoided the balk that dash described in his second paragraph, the runner could be tagged out if he left the base. But even young players are taught to not lead off until the pitcher is contacting the rubber.