Yeah for the xyor part, he (she?) always spawns on the third ship for me. I can confirm that you need to damage phogoth to about 50% health like OP said. I once helped a friend and we were lingering for about 20 mins (all ads killed) and no second ship. Once we started damaging the boss, the 2nd and 3rd ship came and he got this thorn. Im helping another friend out on his first thorn, waiting for him to complete his 500 void kills points. So excited for him to own this beast!