Mounting an optic on top of the carry handle is definitely NOT the preferred way to do so, UNLESS you regularly have to wear a gas mask while shooting (though in that case, a laser is a better solution, IMO).
The reason you see it done by the military is either the gas-mask issue, or because that unit doesn't have flattops. Most military units can't just go changing uppers on their rifles. Lots of red tape involved there.
The ideal situation for either an AimPoint or EOtech is to have the optic mounted forward, over the handguards. Railed handguards work great for this, but if you can't do that, then you can get a gooseneck extension that attaches to the carryhandle. The only mount that I know of that will allow cowitnessing (or the use of the irons at all) with an EOtech is the Ben Cooley adjustable mount. Note that you must be using standard handguards; you can't adjust it low enough with M4 handguards to work with the EOtech.
-Troy