Gigabit Ethernet switch unused RGMII/MII/RMII interface
If it can help to someone. After a while I got the answer from the Microchip technical support. It was unclear for me at the first as I didn't get concrete answer, but after a few iterations I came to the answer that it can be left unconnected if the EMI is not critical. After asking "What to do with unconnected pins if I want to be EMI aware", I got the suggestion to read the following links that can be helpful:
Link1, Link2. I hope this may help someone withe the similar problem.