Eootech by itself (no riser) should give close to an absolute cowitness with standard, A2-height sights. That means the dot of the Eotech will be just about on top of the front sight post with maybe a little variation.
The risers you see all over the place allow for what's called a "lower third cowitness" where the irons are visible at the bottom of the Eotech window, but the dot and the front sight post don't have anything to do with each other.
I had an Eotech with no riser on a carbine with A2 sights. I really liked the setup. The Eotech with no riser is just fine, height-wise and you just select the large aperture and look through the rear sight like it's not even there. We also use basically the same thing on our M4's at work, just with a flip-up rear sight. The dot is near the front sight post, but you just ignore the sight when using the dot.
MI flip up's should be a non-issue as far as cowitness. As long as you can see them through the Eotech window, you should be okay using them as a true backup to the holosight.