You actually have two kind of MACS: an external chip (that can also include the PHY) or an embedded MAC in a processor or FPGA. The TSE is a MAC that is integrated inside SOPC builder.
You have two kind of interfaces between the MAC and the PHY: the MII interface that transmits and receives the actual data, and the MDIO interface that is a slower serial bus for setup, configuration and status report.
In your application the driver is confused because it sees two PHYs through the MDIO interface but has only one MII interface. You could probably configure the MAC to have two network interfaces but I never tried that so I don't know how it would work out.