I agree that stick-shift on its own is not a safety improvement; like you, when I get in a manual car, I shift instinctively. A neatly conditioned response. I switch back and forth between my two cars, one auto, one manual, without messing up shifts in either. The only thing that gets me is my clutch control is a bit flaky for a few days after switching (I run the cars in 6-month intervals).
What I find does help is that my Supra does not have automatic-anything, apart from cruise control. Everything is manual. If I want the car to do something, I have to explicitly set a control to do it. In the process, I'm generally constantly aware of the state of the car, from the lights to the heater. Granted, I did fit parking sensors, but I conditioned myself to never rely on them 100% - shifting into Reverse, I always turn around and watch out the rear window. Even factory-fitted sensors may miss bollards or posts. I have no reversing camera, so I'm acutely aware of the width and length of the Supra when manoeuvring in tight spaces.
I am in agreement that the various electronic driver aids that are sold as safety options are dangerous in the long-term, however. Many cars have automatic braking systems. Not only is this potentially unreliable under certain circumstances, but overconfidence in the system can lead to exactly what the author suggests - the driver's brain shunts authority for panic-braking to the automatic system, without the driver being consciously aware of it, and looks to the next thing on the priority list. Human brains are phenomenally good at outsourcing things. The more we automate, the more we wind up withdrawing attention. Overconfidence in Tesla's Autopilot system is at least partly responsible for the deaths so far (now, I'm not blaming the drivers; they did what anyone could reasonably expect, they shunted responsibility for the car to the computer. No matter how much Tesla disclaim that the driver must supervise the technology and be ready to take control at all times, this isn't going to happen in practise because the shift in priorities happens subconsciously).
There's no clear solution here; the driver aids are set up with the best of intentions, but they may wind up causing more harm than good even to an experienced driver.
And I do choose shift points for economy from time to time :) Sure, sports-shifting is great fun, especially with a performance car, but the only way I can afford to run the car at all is to save fuel where I can, and having full manual control allows me to do that. Roughly 90% of my driving involves shifting before 3k RPM. It's only when joining highways that I let the Supra off the leash :D