Hi @john71,
I understand now. As mentioned on the RM: The "FlexSPI configuration depends on the chip configuration". In other words, it is the chip arrangement that will determine the FlexSPI module's configuration and connections.
To exemplify this, I am using the peripherals tool. Since I am yet to route each of module's signals to a pin, the tool gives me a warning of the pins the module is expecting to use. When setting up the FlexSPI1 module, I am able to select what port of the FlexSPI I will use. Notice how changing the operation port automatically changes the CS pin that the tool expects me to route:



This exemplifies that the SS is determined by the port configuration. Since the evkmimxrt1170_flexspi_nor_polling_transfer_cm7 defines the flash port as port A1, it will use A_SS0_B.

I hope this clears things up.
BR,
Edwin.