NA: How does the EZ FX3 IC decide the clock frequen cy for SPI/I2c protocol- or do they have a fixed frequency of clock which is generated inside the FX3 IC?

Check Schematics Page: USB FX Core.

Pin numbers: GPIO53.

The user guide says:

3.1.2.4  Multiplexing of Address/Data
A GPIF II interface  gives  a maximum of 32 bidirectional data lines, which can be split into,  or time multiplexed with,
address lines. In the case of multiplexed operation, the address bus will have the same width as the data bus. 

Wonder if has any solution to my question.