Nonsense, knee-jerk answer.
First, we don't need all of them to "hold up well to scrutiny" but just 2 (as per TFA challenge). And we have way more than just 2 -- hundreds of great papers.
Second, the papers "that were trying to optimize for bottlenecks in hardware that no longer exist or have shifted to different places" can still be perfectly valid as per the challenge we have, which was:
1) that they were not "full of mistakes and bad reasoning", 2) that they did not "contain little or no original work" (and where thus just references and meta-papers)
The question wasn't if we have "plenty of" papers that are bad, or plenty of papers that were very good but have been super-ceded by changes in technology.
Just that we have at least 2 (and I argue we have way more than two) seminal papers that have original work, and are not full of mistakes and bad reasoning.
Why not? Historians still revere Braudel and The Mediterranean was published nearly 70 years ago. Are you certain that there are no such exemplary works outside of the fields you like?
(What did I learn? I don't remember precisely - it's been 15 years - but I think it was that something on the electromagnetic side was caused by time dilation.)
If the field is not totally vague, then yes. We can still consider certain papers in physics, or chemistry, or medicine, computer science etc. as exemplary decades, or even centuries, later, even when they deal with empirical work.
Soft sciences need not apply.