There are many things there to unpack.
Where do you live where "every single bicycle commuter" has been in at least one accident which is "much worse than an auto accident"?
Can you be more definite about what you're comparing? It seems like you're talking average-case car-car collision with worst-case car-bike collision. The worst-case consequence of an auto accident is, what, the Ibadan tanker truck explosion in Nigeria which killed 100-200 people? And it's not hard to find reports of car crashes which kill 6 or more people.
(For that matter, every walker and runner I know has been involved in accidents, like tripping, falling down stairs, or hitting a low branch.)
There's nothing preventing you from wearing a helmet when you ride. I know people who don't feel safe unless they have lots of reflectors. I don't feel safe when I have to ride on a road with cars, except during the non-rush hours during the day.
The problem about scenarios is they exclude the cost/benefit discussion. I can easily think of a scenario where wearing motorcycle body armor would help. For that matter, I can think of a scenario where wearing a wet suit while cycling would useful - what if you fall into a cold river while crossing it? I could probably come up with a good reason for bringing an air tank - if a tanker car crashes and releases toxic fumes in the air, then you can still breath and get away.
The point of the article was that the cost/benefit calculations for a bike helmet are complicated. There's no clear signal that they are useful. There are scenarios where they are useful, yes, and scenarios where a helmet requirement is a net negative. Both are mentioned.
You say the risks are "downplayed." Did you not read the article, much less its references?
You ask "Should we encourage motorcyclists not to wear helmets?" That's a very different topic. As the article points out: "a recent study identified two broad subpopulations of cyclist: “one speed-happy group that cycle fast and have lots of cycle equipment including helmets, and one traditional kind of cyclist without much equipment, cycling slowly.” The study concluded that compulsory cycle helmet legislation may selectively reduce cycling in the second group."
I am a member of that second, slow group. I bike at about 18 kph. This is slower than the fastest marathon runners. I believe there's an evolutionary argument that running speeds and slower are generally safe for the human body. (Either that, or we need to start putting safety gear on Usain Bolt!)
But motorcyclists and moped riders, downhill skiers and Tour de France riders, all go at a faster rate. The energy in a collision goes as the velocity squared, so there's 6x more energy in someone going 45 kph than at 18. This translates to a lot more possible damage, so more of a need for protective gear.