I had only read the first half of the linked article and what you say is true, the situation isn't as dire as I made out. I would still imagine as a user that if a website told you flash wasn't installed you would think there was an issue with the browser.
Yes, that may surprise users, but the browser will simultaneously be showing in-browser UI asking the user if they would like to activate Flash for this page. The UI should help users seem the connection between the two messages. Hopefully web developers will fix their websites' user of Flash before Safari makes this change (with macOS Sierra in Q4 2016) and Chrome and Firefox in 2017.
