I have a main board with a 10/100 MAC and PHY. This board also includes a discrete magnetics. The board is connected via a suitable high speed board-to-board connector to another board, that contains the RJ-45 port. This port also contains magnetics.
Is there a problem with the signal being "magnetized" twice? The RJ-45 port on the second board is preferred to be with magnetics, because it will be used with other projects that won't necessarily have a discrete magnetic element.