I've noticed this as well. When I'm learning a new subsystem of a code base I learn it much faster when I copy out notes and draw sketches by hand vs. doing it on the computer. I've also found that I can make new ideas gel much better as well when I write them directly to paper.
As a graphics programmer, I'm definitely a visually/spatially-oriented person so I wonder if that isn't part of the explanation for it? Typing at a keyboard seems like a far more symbolic/verbal thing. Firing up a drawing program gets the visual thing back but then it's too cumbersome to be able to keep up with the thoughts as they come.
TFA even mentions one of these avoiding a deer: "You could see the cars avoiding things like a deer that dashed in front of one or another making it carefully around a small hillside road, as a large truck came toward it."
There was also a story here a year ago about Stanford's efforts in this area with a computer-controlled car doing a 180 spin into a tight parking space. "That means Junior could have an entire language of extreme driving maneuvers it could unleash when called upon
Put them together and we're well on our way to computerized control that's safer than the average driver.
To add to your list.
* Blend tool
It's one of my favorites for creating complex highlights and shadows. Inkscape's solution to that seems to be blurs, but those are rasterization effects and bloat the size of any PDFs I export. I prefer all-vector solutions when using a vector graphics package. Admittedly, there's a bundled plugin to blend paths, but it's always been very crash-prone for me. Worse, I can't easily just tweak the result just by modifying the key paths like I can in Illustrator.
* Layer window
No, the XML tree outline is not the same thing.
Aside from changing indentation, I've used it for things like turning single column tables into multiple column tables, removing common prefixes from a list, removing commas from aligned numbers, moving table columns in LaTeX source, and moving pieces of ascii diagrams around (for block comments designed to be renderable in ditaa.) Those are just some uses that I can think of off the top of my head.
I find it one of those things that doesn't seem very useful until you have an editor that can actually do it. Then you suddenly start finding uses for it.
Others, off the top of my head:
Sony Imageworks has started to open source a series of components recently. Admittedly, some of them like Pystring are fairly minor, but others like OSL are serious pieces of code.
Disney's Ptex library is also open source.
Then there's the old Cinepaint project from R&H.
It's not as though they're competing for a prize here. It's just a friendly competition. You're free to ignore their result and focus on the rest if you like.
Personally, I find this kind of thing interesting as far as seeing what's possible, even if it's not exactly practical.
Always draw your curves, then plot your reading.