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I would never mount an optic above the irons because the focal plane is too high above the bore axis. There are a lot of Aimpoint goose necks on EBay for about $10. I have one that came with my CompM4 but haven't tried it.
If you have other flat tops with scopes then why not keep this one configured with basic iron sights?
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Personally, this is all very relative. If you shoot any other kind of traditionally stocked rifle, like a shotgun, or a bolt gun that doesn't have a monte carlo comb, they drop and are much more generous than the cheek weld on an AR. I think AR's sight height to cheek weld can become pretty tight. Especially with certain stocks. I've tried some stocks that are just so uncomfortable to me, because I feel like I'm embedding my teeth, through my face, into the stock. I have this with the CTR.
I think something a little higher than a stock AR height is perfect. A lower 1/3 Cowitness height is a really nice height. And some optics on the carry handle, if low enough, are really not bad at all. "Too high above the bore axis" is just a matter of opinion. There have been plenty of dudes that went into harms way, using some kind of sight on top of the carry handle. It might not be ideal, but it has it's benefits too. For longer necked people, it might even work a little better. Head position is more upright. Sometimes a normal height AR can get peoples head too far forward, looking through the sights with your eyeballs in a drastic, looking upward position and that's not really optimum either.
It's just not as bad as some make it out to be, in my opinion.
I have an ARMS #2 mount and you can mount anything on it. I have shot a lot with an optic on a carry handle in some way and I've never found it to be a bad thing. I have had some really good results, even shooting for groups with this type of a set up. In all honesty, I think a height somewhere right in-between stock iron sight height and a scope on top of a carry handle rail, is optimum. That's just me.