This headline/article are pretty misleading. It makes the issue sound like if you had "Protect My Tweets" enabled, your tweets were still public.
From reading the original notice [https://help.twitter.com/en/protected-tweets-android] it sounds like the setting would just be disabled, which then made your tweets public. But not that Twitter's app would continue to say they were protected. That's a pretty significant difference (also by the fact that such a huge thing was not noticed for 6 years I'm guessing not many people were actually impacted)
Also just for fun, I'd wager how it happened is that the developer had some "default request object" that had "true" as the default setting for this and merged it with the updated property values ;) a classic