I have designed the processor pinout using GPIO38 as MII_RXD2 and GPIO46 as MII_TXCK. This is fine based on the technical reference manual and the pinmux utility. I have discovered that the datasheet states that functions are not available for these two pins, therefore they can only be used for general purpose IO or USB functions.
I need to find out what is real story with these two pins. I am ready for layout but if I have to move these two pins it will take a significant amount of scrambling to get the functions I need.