I hope this makes sense to you…
The Eotech is a reflex sight, meaning you can look through the window at any angle and if you can see the dot it will be on the point of impact. The dot moves as you move your head, so it always lines up to the point of impact. The front sight does not move; you can only line up your irons one way for point of impact. If you move your head the fixed front sight will no longer be on point of impact, but the red dot will move to stay on point of impact. This is all in relation to your point of view.
So yes, by design the sights can be misaligned per say. If you zero everything together, when you look through the irons the dot will align with them (true or 1/3 co-witness). When you don’t look through the irons the dot will move to align to point of impact. In any event you can just move your head so the red dot lines up with the front sight post. If you adjust the windage on the irons (usually only adjusted on the rear sight) you will have to adjust the windage on the eotech also.
In all reality it comes down to how you feel most comfortable shooting, not how cool your rifle looks. Try it, you may never notice the front sight and block it out of your vision, it may annoy the hell out of you. You can always remove the front sight afterward. Many people run Eotechs with A2 front sights; it has its advantages and disadvantages.
This got longer then I intended… but I wanted you to be clear on what is happening here. If you have any more questions please ask. Maybe look up the wiki for Reflector Sight and look at the little animation…