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It's kinda crazy that this is the format we've standardized on to carry all of the output of academia into the future.

Actually, it’s not. The archiving standard is PDF/A, which is (as I understand it) much more structured and standardized.

A lot of the input is LaTeX, so that's ok.

And arxiv asks for the original latex source when submitting.

Well, at least, pdf is probably better than printed paper for that purpose.