For Spartan-II/-IIE, are the I/O clamp diodes enabled during the configuration process?
No, they are not.
The Spartan-II device is 5V-tolerant during configuration with no external modifications. If the Spartan-IIE device is subject to external 5V signals during reconfiguration, a rise from 3.3V to 5V caused by the disabling of the diodes might occur on the I/Os. You do not need to be concerned as long as the current going into the I/O is limited using a resistor connected in series between the external signal and the Spartan-IIE I/O. Please see (Xilinx Answer 8654) for more information.
For more information on which I/O standards utilize clamp diodes, please see: