Please do not connect any other pins which marked as DNU.
In other words, shall ALL these pads remain strictly unconnected? Maybe a subset can be freely connected?
>> Please do not connect any other signals to the pins which are marked as DNU.
I suppose all unconfigured GPIOs will stay high-impedance during all stages (power-on, boot, run), or must I expect spurious transitions?
>> Please refer to section 11 of the application note AN76405 https://www.cypress.com/file/201991/download which mentions the default states of the GPIO's of FX3. Similarly, for CX3 the GPIO state might differ based on the boot option. Please try probing the GPIO's for the default state (while in bootloader mode)
Please let me know which kind of signals are you trying to pass through the unused GPIOs