I was curious whether there is an  ML3 mount that adapts to both flat top picatinny-rail recievers as well as A2 carrying handles? if not, can someone suggest a good carrying handle mount that allows co-witness with the iron sights?

Aimpoint makes the M68 package which is used by the military that consists of:
Carry handle mount (gooseneck)
QRP mount
QRP spacer

This allows the issued operator to mount the Aimpoint on either a flat top (using the QRP and the spacer) or an A2 (gooseneck and QRP w/o spacer).

There are also numerous other manufacturers, ARMS for one, that make lots of other mounts that will also do about the same thing.  I currently have an ARMS 39 mount on my A2 with a QRP and my CompM.

If you are looking to mount the Aimpoint on top of the carry handle with the same mount used on the flat top then there will be a problem.  A flat top mount is taller (to clear the front sight base) and if that mount is used on top of the carry handle it will be extremely high and difficult to use.  

Hope this helps.

Sarge