I agree, in that I don't like a red dot field of view that is obstructed by iron sights right in line with the reticle... however the co-witness with the Troy/NEA rail would be a lower 1/3 co-witness. You can basically use the red dot above the iron sights, and if the optic fails, the iron sights are right there, without removing your optic.
With the optic mount that you suggested, you completely off your rear sight! A setup like that is fine on a flat top AR, where you have pleanty of rail space for a flip down back-up sight, front and rear of the optic.... but what the hell good is your rifle without an iron sight?!