The USB packet formation is done by the USB PHY(hardware). It is not advisable to change these fields on fly from the firmware.
Could you tell why do you want manipulate these fields?
I am working on a product which sniffs and parses USB packets (including protocol layer), and controlling these fields is essential in order to test it.
Is there any way this can be achieved using the FX3 ?
It is not possible to do so, as these IPs in FX3 work on par with the USB Specification. Manupulating these fields will be in violation with the USB Specification.