I have come to accept that some systems are better run on paper than on the computer. Whenever I am required to develop a new system or routine, I do it on paper first. If I go to a computerized system first, it will be how I think it should work, rather than the way my/our brains really work. I find that once I have been running a new system on paper for a while, then I know how I want it to work on the computer and can develop it accordingly. This may be something like tracking stationery orders or courier deliveries, phone logs, file recalls, weekly accounting reports, etc. I don't really know how my brain works and what is required until I have been doing it on paper for a while. Then I can morph it to a computer system or computer + paper system that works.
I have also come to realize, as do the authors of these articles, that paper is an important tool, especially when collaberating with others. I may feel quite comfortable annotating or amending on the screen, but when it comes time to share my work with my boss, it needs to go into his paper in-basket, not his e-mail. It's just what works. It can be quickly handled and turned around.
I disagree, though, with calling orderly piles of paper on a person's desk "clutter" or with equating loose paper with clutter. Yes, my desk is clean when I go home, or has one or two items which must be handled immediately the next morning left on it. All loose papers get coralled in folders, but a file is just a "pile" that is mobile. I can move it on or off my desk with little effort. It can be in my office, my boss's office, or the file shelf. I do stack things and make piles throughout the day, but at the end of the day those piles get put into files or sub-files so that they are easy to find and access.