Maybe cowitnessing means something a little different than you understand.

The concept is that iron sights shoot to a certain point of aim, point of impact. Cowitnessing simply means that the red dot also covers the same point of impact as the iron sights.

Thus, as you correctly stated, you use one or the other, generally ignoring the iron sights and using the dot. Either system will give you the same PoI.

If the dot fails, the irons still work.

Usually you want both front and rear irons when aligned to protrude into as little of the bottom of the RDS window as allows them still to be useable. That is usually from about 20% to a max of 30%. You don’t want the irons to occlude the RDS window any more than necessary. You control the protrusion into the window by the height of your front and rear sights.

I hope that helps. There is more to using an RDS than just cowitnessing, but it is a feature that is sometimes discounted or misunderstood.