I think a good part of the reason they never addressed this is that there’s no good answer. Any answer that posits it to be impossible that I can think of comes with awkward connections to the idea of a ‘soul’ or some such nonsense that makes duplicates non-viable, which I’m sure they really didn’t want to introduce.

After all, it’s not like transporters were part of a well thought out extensively considered backstory when they were first introduced. As I understand it, the issue was they didn’t have the budget to keep shooting shuttlecraft scenes in every episode, so they came up with a way they could get the characters to the planet without having to use a vehicle in most situations. This decision has had its upsides and downsides, but I think on the whole, it has created far more issues than it ever solved. This is far from the only plot point that has issues in order for story to work with transporters. And considering how often they encounter situations where the transporters don’t work, from an in-universe perspective the technology seems…unwise…to use on exploratory vessels.