[militarymoron]

hey woob, how's it going, dude?
when it comes to co-witnessing irons and a dot/reflex sight, by definition if you can look thru the sight with your irons, they'll be co-witnessed already. i.e. if you line up your irons, the dot WILL be centered on top of the front sight post.

now, if you move your head away from the irons, the dot will no longer be co-witnessed, but it'll still be on target (since it's parallex free - which means the dot does not have to be centered in the tube).

being a civvie, and not being in fear of being attacked by cardboard sillouettes, i preferred a clear sight picture thru my aimpoint or eotech so i had flip up front and rear sights, which i kept down when shooting 'normally'. i disliked the irons cluttering my my field of view. but then i also started shooting with them up, with and without the sights turned on, to get used to them also, and i found that the sights 'disappeared' as i concentrated on the dot.
flipping sights up and own is a luxury that you might not have as a 'real world' user (which i most readily admit i'm not) and is probably not the best way to go.

woob, i think your buddy's reflex on the carry-handle mount is centered on the irons. combined with the relatively small reflex lens way out front, i can see how it'd be a bit distracting.
IMHO, the way to go would be to have fixed front and fixed rear sight (like a LMT or cut carry handle). mount the sight (eotech or aimpoint) so that the irons co-witness in the bottom third of the tube/window (instead of centered in height). when the sight is on, you're looking over the irons, and using the dot. if the sight goes bust, you just lower your eyes a half inch and use the irons. no flipping sights up or down. just my .02.
BTW, i know that guy in the Army with the BDUs. and chen, too.
cheers,
MM