I really don't think it happens that often, and HTC does not allow an IP address to have two counts (as far as I know).
I'm not a big fan of this idea because people will be mistaking friendlies for enemies, just like in the FSO. Now if the FSO this is generally not a problem because everyone always coordinates their tactics like in reality, in the MA most people don't do that. Don't get me wrong it's a good idea, I personally just don't really like it.
Just for the record, IFF existed during WWII.