Are there any ways to specify GPIO + GPIF operation without having to specifically override the functionality of the GPIO's that end up as part of the UART?
How many GPIOs you are looking for.
You can use I2C (GPIO58-59), I2S (GPIO 50-52 and 57) and CTRL lines (GPIO17-29) as GPIOs as well.
Please let me know the exact requirement of your application and I can help you better.
You can also refer to the "Pin Description" section in the FX3 Datasheet.