The most typical usage of the MDIO Interface component will be in modules that implement the CFP MSA Hardware standard for 40 Gbps and 100 Gbps optical modules. The specification for those optical modules uses the MDIO interface standard for management of the module. This type of equipment can benefit from a programmable solution to implement this interface and a description of that implementation is shown starting on page 17 of the Data sheet in the Functional Description. The previous page has references to the applicable CFP MSA Specifications. For this very high speed equipment the data traffic certainly will not be going through the PSoC device.
For standard 100 Mbps Ethernet data interfaces that you describe (MII/RMII) the MDIO interface for those connects to the Ethernet Phy and would already be integrated into those devices.
There has been some discussion in the forum about support for 10 Mbps Ethernet support directly in PSoC (Ethernet Component). That work is ongoing.