The case book is somewhat ambiguous about tagging the base. For example, B/R beats the throw but misses the base. F3 is still standing on the base when the throw comes in but F3 makes no indication that he is appealing. The call is still safe until you recognize that F3 is making a deliberate appeal. It's a fine line but since the "accidental appeal" has been banished, you have no option but to signal safe until F3 demonstrates an appeal. As earlier said, why would you reward the defense for a late throw? The intent is that the defense must RECOGNIZE that the base has been missed and then properly appeal.