Consider that it’s also now true that “normal” incidents among the 100k+ daily commercial flights are now newsworthy if they involve a Boeing plane, when they wouldn’t have been a couple of years ago.
You’re still far safer in any commercial flight than walking the dog in your neighborhood.
I can't read that article, but I'm assuming (hoping?) that even if the software is flawed, there's still clarity about which source code / build configuration is installed on a given plane.
Contrast that to the allegedly faked test results, and known defects, of the planes' physical characteristics.