What we're trying to say is that that approach does not work so well if your individual files are 1-2 orders of magnitude larger and your whole analysis dataset

What we're trying to say is that that approach does not work so well if your individual files are 1-2 orders of magnitude larger and your whole analysis dataset (which must be processed in its entirety to answer any question!) is 4-5 orders of magnitude larger. Yes, not everyone has such large data sets. (And not everyone has such small data sets!) But it is imperative that scientific computing infrastructure developers understand what classes of experiments they are serving, and what classes they can not or should not serve.