I'm in need of remoting the gigabit ethernet connector from the main board to a back end board that has all the other connectors. I plan on doing this with a high speed board to board connector (Samtec QRF8-026-05.0-L-D-A-GP which has a ground plane and using extra pins to separate the differential pairs), but I don't know if it is less damaging to signal integrity to remote the PHY from the magnetics and have the magnetics in the same board as the connector (built-in magnetics are not an option), or have the magnetics on the main board and remote the connector alone. This is under 1.5 inches of remoting overall.
One restriction is that the board area in the connector board is very limited.
I know that ideally they should all be on the same board but remoting the connector will help a lot in the overall design of the product.
If at all possible, please explain your answer in terms of the physics involved.