The one thing I don't agree with is how the writer argues that, because the UI elements like the "+" button are red, it means they might be misinterpreted as performing a negative action. I think it's not a good point because it's easy to tell that red is the accent color of the application (for example the active navbar button is red), and thus it doesn't really play a role in telling the user whether the action is a positive or a negative one. The fact that the big round buttons start as green, and only become red once tapped (along with a change in their label), should make it easy to tell that they're not red because it's the accent color of the app, instead they're red because they perform a destructive action (in this case, resetting the timer). Their label further confirms their purpose.
As a last remark, I don't think that even the least savvy users are to be treated as "dumb". If they care enough, they will figure it out nonetheless. This isn't one of those issues that would make it impossible to use the app. You just need to put a small amount of thought in using it.