On my wife's CZ Compact the dot of the DP Pro is right smack on top of the fiber optic front sight. My wife finds it confusing but I thing she just needs to shoot it more. And, were the iron sights be necessary to use it would most likely be that the red dot had "died" anyway, either through dead battery or malfunction.
On my RMR equipped CZ P07 and P09 the dot is somewhat above the top of the front sight. Sounds like what you described, the back up sights are in the bottom of the lens. Now I don't mind that. If the dot is centered in the lens (doesn't have to be with the RMRs - not sure about the DP Pro, yet) the iron sights are easily visible in the bottom section of the lens.
In my opinion, you train for the good times (red dot working) and the bad times (switch to irons as if the dot had died) and after some practice you'll do it without thinking about it.
I've said this before. If I lose/drop my glasses I cannot see the front sight. The sights/top of the pistol are just a big blur. The dot is a fuzzy dot, but I can see it. It's not too hard to put a fuzzy dot on a target that I can see.
There may be another red dot pistol, or two, in my future.