Except configurations have a position, that's part of a configuration, and even something identical in all other parts of the configuration cannot be identical in the positional aspect, if it occupies exactly the same point in all dimensions and fits all other parts of the configuration then it is not a duplicate identical particle, or whatever the configuration represents, but the same thing. There's not two of it, there's just one.
With that in mind, that two things don't have the same positional tag two things can never be identical, without being one thing.
Atom X has configuration of 4, 3 in substance, and 1, 1, 1, 1, 1 in position. Something with the identical substance 4, 3 but of position (say 1 second later) 1, 1, 1, 1, 2 is not identical, it would be classically, but not with configuration.
Atom X 4, 3 substance 1, 1, 1, 1, 1 is identical to Atom X 4, 3 substance 1, 1, 1, 1, 1, because it's the same thing, but apart from that everything is completely different and unique. In fact, if they weren't you wouldn't be able to distinguish them to talk about them, if Electron 1 and Electron 2 is really Electron 1 twice you wouldn't be able to test for them separately or do anything to one that you couldn't do to another (like separate them as in your example). In fact, with your example you start of with two fundamentally not-identical things (by the fact that they both go to different places in different amounts which identical things would not do).
Think that's all.
What was the purpose in tasering the Captain? It seemed a needless mutiny since all he had to do was let the Captain know of the possibility, he obviously hadn't thought about it after all.
Why the hell did the SuperHappy or whatever people not predict that? Unlike the humans they know everyone is capable of destroying the sun and starlinks, so without question they should have predicted that in the face of total domination from both the BabyEaters and from the humans. Why did the BabyEaters destroy the Star (and so the links)?
This seems a uselessly temporary measure since stellar events are going to happen and over long enough time scales regular travel will be possible between stars.