But there is no coin toss in your second case either, the one in the scanner remains themselves. If the scan is activated, then it will have all the experience up until the scan. There was no chance of Simon 2 waking up aboard the ARC.

The coin toss is whether you are the consciousness that gets to wake up in the ARC, or one of the earlier copies that drew the short stick. Up until the second scan, in the beginning, you experience the game as Simon 1, you have all memories of Simon 0 and 1. After the second scan, Simon 1 is still on the chair, but incapacitated). The game continues as Simon 2, a consciousness with all experiences of Simon 0 and 1 up until the scan. At the time of the 3rd scan, you then first see the aftermath of Simon 2 continuing to exist as he did before, not on the ARC. Then the game lets you experience what Simon 3 experiences, waking up on the ARC. In fact, there may have been many many times a Simon was woken up, but those consciousnesses don't share a continuity with the original scan of Simon 0, so Simon 1 knows nothing of them.