I’d kill for a game with the scope of Skyrim where the NPCs truly felt like they were living their own lives.

In practice, I agree with you. The transporter scans, disintegrates, and reconstructs the thing being transported. But when the thing being transported is reconstructed at a subatomic level it is effectively identical.

I can imagine the society we see in startrek having already worked through the moral and philosophical implications. I would have loved to see that addressed in an episode tho.