The Nature preprint references this zenodo archive with data and code in a big 13GB .tar file: https://doi.org/10.5281/zenodo.13158382

I haven’t downloaded it to see what’s in it.

As another comment mentioned, papers get revised during review, usually in response to reviewer comments. Also, some journals (not sure about Nature) do not allow authors to "backport" revisions made in response to reviewer comments to preprints; I guess they view the review process as part of their "value add".

Its quite common to revise papers. For example, they might have uploaded to arxiv in order to submit to a conference. Later, they revised and submitted to Nature.

Arxiv is mostly meant for preprints for peer review.

In a Nature paper in particular, the final layout is typically done by the journal's professional production team, not the authors.

Not all publishers grant permission for authors to upload the peer-reviewed and layouted postprints elsewhere.