A bit more thought on the subject. The LAN filter chip as I mentioned before is meant for 4 100MBit ethernet interfaces. 100MBit ethernet over UTP only uses 2 pairs, i.e. 4 wires. The way the LAN filter is wired up on this board, the gigabit connection (which uses 4 pairs, or all 8 wires) is routed through the LAN filter as though it is 2 100MBit interfaces. This way 4 pairs go through the filter and half the capacity of the filter is used. It could still filter 2 x 100MBit connections or 1 x gigabit connection.
If you look closely below the LAN filter chip on the first photo in this thread you can see there are a bunch of surface mount components missing. This is the 'out' side of the filter - the LAN interface connects to the top of the chip which is 'in', then 'out' comes through these components before connecting to the SoC. These components are missing for the left half of the filter's 'out' connections, so the additional RJ45 connector I soldered on was never actually connected to the SoC. For an enthusiast to add the 2nd ethernet port, at least these components would need to be present, which is well outside of the realms of most enthusiasts as I think I have proven today with my de-shielding technique
I do have access to a PCB shop that could do this surface mount stuff for me but it seems a little pointless - very few others will have this so it doesn't benefit the community. I will still lift the flash chip and see what's in it though.