GPIO 16 is used for clock pin. This can operate up to 100 MHz.
It can be clock provided to FX3 by external processor (FPGA to FX3) or FX3 providing to external processor ( FX3 to FPGA).
Rest all pins are used as Control and data pins.
You cannot use GPIO 27 as a clock, which is similar to GPIO 16.
It can only work as a control signal. The frequency of the GPIO 27 depends on state change in GPIF II SM.
There is no relation between GPIO 16 and GPIO 27 (any other GPIO).
i.e. In the attached interface (by you), the GPIO 27 output can be changed as per the states defined in GPIF II SM.
This can be defined as per the FX3 FPGA interface requirements.
Thanks a lot !
Definitely it gave me hint and now I can understand. However, still need to study more on this from FX3 TRM.