Interestingly Erspamer doesn't mention any prior history or traditions of this sort of practice, just that it works for creating theses within the humanities very well. How does he miss this as motivation?

Presumably for him it's a "cultural practice" and Eco delineates it well. Erspamer learned from Eco and it's just what he does... The only questioning done is how 90s technology fit into the picture and that was only surface level questioning...

There's definitely something off about this as a recommendation for the overall system.

Esparmer is correct that research and writing did change with the advent of word processors and the internet in the 1990s and early 2000s (p xi), but these were primarily changes to the front and the back of the process. Esparmer and far too many others seem to miss the difference in which affordances were shifting here. The note taking and organization portions still remained the same, so Eco's advice is still tremendously important. Even if one were to do long form notes in notebook format or in digital documents, they would profitably advised to still properly cross-index their notes or have them in a form that allows them to rearrange them most simply with respect to the structuring and creative processes.

Losing the ability to move ideas around easily, restructure them, link them together and outline them was a tremendous blow in going from the old methods to the new digital ones.

Did we accidentally become enamored of the new technologies and forget that their affordances didn't completely replace those of the old methods?

In 2015, when considering Umberto Eco's use of index cards in his classic book How to Write a Thesis, Francesco Erspamer comments that taking notes using index cards was more common and even nostalgic for those who attended college prior to 1990