I think the main point for the run scoring was that TOR did not tag 3rd base to make that runner out before leaving the field. It would not really need to have been an "appeal", they just had to tag 3rd to make that runner out. But in that situation, I don't believe the runner is automatically out. The defense has to get the ball and tag 3rd base for him to be out, whether in the course of the play or by appeal. Until the defense does that, it remains a live runner.
So in this case, that runner was never put out at 3B by the defense, the runner reached home before the 3rd out was made at 1B, and the defense did not appeal anything before leaving the field. Very strange sequence of events for sure.
Think of it if the runner on 3rd did tag up but left a hair early, and scored before the 3rd out at 1st base. It is kind of the same thing. The runner would be ruled safe at home if he got there before the 3rd out. The defense would then have to appeal the play at 3rd to have that runner deemed out and void the run (the 4th out). Same thing except the runner left really early.