With the BUIS forward it gives you more realestate. While nothing is there on my personal gun, my work gun has a PEQ23 there. There isnt enough room to even change the battery between the EOtech and the laser with the BUIS facing backward. It may not even have fit, I dont really remember. Either way, turning around the sight just gives more room on the rail and it still works the same.
The Eotech issue was fixed as far as I know. The problem w/ the 553 models were not the battery compartment iteself it was the rubber and cheap metal used where the body and battery compartment meet. (this is basically what I was told by Crane, the guys that tested and developed the program). I like looking through a window instead of a tube. It allows me to shoot both eyes open much easier. As I have said before, just train with whatever you choose and you will be successful.
I like the glass and the eye relief on the Aimpoint magnifier better than the EOtech. Mostly personal preference. If you use the setup I have you will need the spacer in the magnifier mount to bring it up to the correct height.
Hope this helps!