Entrei em contato com o Prop Master do filme e o filme é Senior Graphics Artist que gentilmente respondeu ao meu (mais que um pouco estranho) e-mail.
Eu assumo que eles não se importarão de eu citar textualmente.
I don't remember any 4 hole binders. We punched all the hand books to 3 holed ones with 2 hooks like NASA does. The binders in bg [background] were probably 4 hole just cause it was easier to get. No hidden meaning just budget and time. Haha
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There are many prop elements that go into a complicated film like the Martian and when making decisions about what props should look like we firstly research what NASA has used in the past, or what fits into are fictional Martian world and helps to tell our story and look good on screen.
I'm pleased that you and your friends found the ring binders so interesting, I just hope the rest of the film lived up to your exacting standards.