“Natural breaks” are when the Mac is not being used; idle.

By default, Time Out will wait briefly then count backwards when you are having a natural break, to give you credit for not using your computer.

If you do a lot of reading on-screen, that doesn’t cause keyboard or mouse activity, you can change the app to disable this behavior by choosing Continue Countdown from the popup menu on the Break Appearance page of the settings.

Or if you’d prefer to have it just pause the countdown, instead of counting backwards, or reset the timer, those are also options.