Well, I've run a TA11 ACOG on both a fixed A2 carry handle and on a flattop.
Unlike several here, I did not feel that the ACOG was too high on the carry handle. In fact, I thought it worked pretty well up there. The height over bore for the TA11 ACOG is only about 1" higher than the height over bore for the iron sights. The compact ACOGs sit even lower in the carry handle.
I was using an RRA Enhanced telestock at the time and didn't feel any need for a cheekrest. You will end up with more of a jaw weld than a cheek weld but since I use nose-to-charging handle as my reference point it did not effect my shooting in the least. In fact, it was easier to move and shoot with the ACOG mounted on the carry handle than it has been with it mounted on the flattop.
Another nice feature is that your iron sights are instantly available and several of the ACOGs are designed for the carry handle so there are no vertical parallax issues.
However, I ultimately went to a flattop because there were some issues with a carry handle mounted ACOG.
1) Cases, gun racks, etc. are usually a tight fit for a plain AR15. Put a scope on top of the carry handle and the rifle won't fit in many of them.
2) No reliable return to zero with a carry handle mount. Every time you remove the scope, you need to rezero the weapon
3) Difficult to clean the rifle without mucking up mounted scope unless you remove the scope, see #2.
Also I'd advise against buying the cheekrest for an AR even if you do decide you don't like the height of the ACOG. The cheekrest will make irons unusable and the money you would spend on one would probably cut the price of a new flattop upper in half (though you would still need to buy a good flattop mount).