Hi Zac,
The short story is the TWR-SER card is being setup for RMII mode which reduces the number of Ethernet signals required.
The TWR-SER card is also sourcing the 50MHz clock to the PHY and it gets jumpered to return to the MCU/TWR-K60D100M card. The MQX RTOS software configured to use external 50MHz clock signal as the MCU clock source.
With both the MCU and PHY being clocked by the same source, the clock domains are the same and the TXCLK and RXCLK are not needed.
Hope this helps.
Regards,
David