If I understand you correctly, you are going to configure an external PHY via MDC, MDIO bus. In that case you have to use eTSEC1 MDIO memory-mapped registers, even if the PHY is connected to eTSEC2 or eTSEC3. This is because MDC and MDIO signals are TSEC1 controlled. Make sure that PHYs connected to the MDIO bus have different bus Addresses.
eTSEC2 MDIO memory-mapped registers should only be used to configure internal TBI PHY, in a way described in section 15.10.1.4 of the Ref Manual.