The fundamental difference between your two positions seems to be that an identical ship that was created would be a fundamentally different ship. But that’s just something you’ve assumed. Why would that actually be the case? What, when you really get down to it, would be the difference that you could point to and say “ah, this one is a copy”? They would be, truly, definitionally, the same object. The differences between an original and a duplicate that existed together would only appear after they were created - if they appeared before they were created, then (again definitionally) they wouldn’t be identical copies.

If you destroyed the original and then created the duplicate, there wouldn’t be any differences - it would be created as an identical version, and continue being that version, accumulating differences only to itself. Nothing about it would have diverged from that instant of creation. How could it? There’s nothing to diverge from. If you can assume that there could be an original that isn’t destroyed, and then a copy created of it, then why couldn’t you just swap those labels around? Have a duplicate, and create an original from it. If for an instant they’re the same, then… er… there’d be no difference. The labels are just be a human affectation.

Think of it like transferring a file. I’m sure you’ve moved a file onto a different drive or dragged something from your downloads folder to your desktop or somesuch similar action. What actually happens is that the file is frozen to modification, copied from one place to the other, then deleted from the first place. But in all the times you’ve done that, have you ever thought to yourself “huh, you know, this isn’t actually the same file as what I initially clicked on”. And that’s because fundamentally, mathematically, it is the same file. Changes to the file follow it around when it’s moved again, if you change the name it’s still referring to the same piece of data, etc. It’s the same, single file.