Just because you can see through the rear window doesn't mean you will see the dot.
In unconventional positions and one handed you can't rely on your index like you can in a conventional 2 handed standing or seated position.
When you use Iron sights you are always using your peripheral vision to help pick up and align the sights, whether consciously or unconsciously. This is where the "scope shadow" of tube sights like Aimpoint Micros and ACROs or semi tube sights like the SRO is useful. The new Holosun with Vulcan reticle uses the same concept.
Using co-witness to find the dot is doing 4 things vs doing 1 thing. Unconventional positions is one of the few times it can be useful but still sub optimal.
The other issue is how much of the tiny window is taken up by the front sight ? My initial dislike of the RMR was based in part on the fact that the True co-witness BUIS took up half of what was an already small window. A switch to 1/4 co-witness BUIS made the RMR much more usable.