Well, if you're talking about the Andromeda thing with Annie and Luna, I don't agree for this particular point, as it was highly implied that the sector was evacuated and there was nobody else left on this planet (well, except a certain people looking for nests, as we learned later). If there was still people there, either players or NPC, they would certainly have been killed by Xenomorphs soon after anyway, so the spell didn't change anything. Was more something like “desperate situation” than “free violence” at this specific point.
For your second point, Orion explicitly said that Dione was bound to Nova just as the Gems were bounds to him at the time he was talking about them at the very beginning. But I agree it's weird that it's possible in Eternum with real bodies but not in “the real world”, I'm waiting to see how the story will deal with magic in the next chapters.
I also agree they should have go back to “the real world” before going to the ship (thought about it while playing), but that didn't look too weird they didn't, because it felt like an understandable combination between “need to hurry before the island disappear” (wouldn't have been that long, thought) and “too excited by the situation to think about what would normally be obvious”.