Pagination or not, both pagination and files provide some degree of spatial sense just as 'loci' and memory palaces.
Edit addendum:
There are theories about which senses are our dominant ones, and how they affect our learning processes. Some may lean towards visual ques in their mental life, others on kinetic or sound. Personlly I experience my mental models as spatial. Even abstract thoughts become situated "somewhere", if not by itself, then by contrast of other things on my mind.
"Everything is a Memory palace."
Needless to say, when I'm deep off in a terminal with something, I don't think I'd describe it as text-based.
I.e. we strive for short functions, we use indentation heavily, it is commonly rendered in fixed-width fonts (this helps with spatial memory/overview too), etc.
Which also seems to align with the article's description of how it works: you're not trying to figure out the underlying structure of what's going on, you're making up a new structure as you go based on the surface-level patterns.