Possible to have too much magnetics in Ethernet
The topology you have listed is a little difficult to understand. The proper way of doing this is to make sure you have a phy on each end of the magnetics.

This is how I would consider designing the system:

If board 2 is simply a pass through:  

Board1 phy-> diff pair 100Ω and 100Ω connectors->board 2 -> magnetics -> cable

OR put the phy on board 2, it will increase the conductor count on the cable, but might be a better option as the phy's signals run at slower speeds.

Board1->phy on board2->magnetics ->cable

If you are doing anything with the signal on board 2, then that will probably violate the 100Ω impedance (you can't split a transmission line easily.)

Also a typical ethernet channel has one transformer per line and one choke. 

Check out these questions:
Connecting two Ethernet PHY without magnetics?
Connect two embedded devices with USB host with Ethernet?