Here's an example of the red dot with a 1/3 mount on a carbine set up for training classes.
Red dot is centered in the window, zeroed and dead on at 50 meters. The iron sights are visible below the dot, in the sight window. They also zeroed for 50 meters.
The dot is centered in the window, much like a peep. The difference is that you can cover the front of the red dot optic, and still shoot with the left eye open, and "see" the red dot on your target.
OP - you probably have a strong dominant right eye. Your brain is trained to look at a tube and at sights on a rifle in a certain way, it's going to take a while to "unlearn" looking through a red dot like it's a scope.
With the irons lined up, the red dot - still zeroed- lines up with the irons. If the dot fails, the irons are still visible to shoot with. I've got a bit of cant, juggling the phone camera, and the rifle, but you get the idea.