@User: There are two sets of registers, one in the management SoC and the other distributed around the padframe. The "transfer" bit copies the data from management SoC to the padframe. If you read back from the location where you wrote the data, you will only confirm that the data are correct in the management SoC, not that the data are correct in the padframe. The only way to confirm the values in the padframe is to set the state of the GPIO to output and apply a value. If you apply some sort of slow toggling value to all the GPIO outputs, then you can immediately probe which ones are set to input or output.

Thank you for the explanation