Off the top of my head: Maya, max, and xnormal are not synced to UDK, Source, Unity, or CE3. Not sure about Marmoset. I know of a few engines synced to maya but they are only being used in house. I have never baked for idtech but it is my understanding that they have their own baking tools and everything syncs correctly.…
When most of these game engines and baking tools were written, few artists were actually baking anything other than characters (which are usually a little more forgiving). Also, all of these engines already had code for handling normals and I would guess the normal mapping stuff got tacked on.