I am pretty sure the first run Magnum engines did not have the truck mounting bosses in the block, only the old style LA mounts. But all later Magnum engines from the trucks people call "first gen" from 1994 on do have the truck bosses because that is what they used.
I have a 1993 D250 truck with it's original 5.9 Magnum engine still in place, and I know the history of this truck. I will have to double check it to be certain, but I am pretty sure it only has the old LA style lugs. It will be at least this weekend before I can check it.