If they’re old enough and rare then copyright is moot, as you mention. The size of the vault is of interest but it’s not something that makes the vault possible vs impossible.

I’m not a lawyer, but I would guess the theory behind the destruction is to guarantee that they are authorized under fair use to have and to use their digital copy. Imagine a situation in which someone else becomes the owner or is using the original. If you destroy it, that becomes impossible. If that’s part of the constraints, then a vault, rather than a library, could be a key distinction.

You might be confusing the need for an original work that draws upon another to be “transformative,” in order to not violate copyright, with the notion of “fair use,” which allows scanning something you own for your own personal use.