The BitGen option "Persist" will allow dual purpose configuration pins to remain as dedicated configuration pins after configuration completes. This option should pick up the "config_mode" constraint which allows the software to set up the device and files properly for the configuration interface being used. This option should persist the configuration bus specified by the configuration mode constraint. The software will only persist the 8 byte wide interface, even when the configuration mode constraint is set for x16 or x32 mode.
This issue will be fixed in 9.2.02 and BitGen will apply the correct persist settings for the x16 or x32 modes.
In the meantime, the -g option in BitGen that forces the interface to persist is as follows:
16 bit persist: -g persist:x16
32 bit persist: -g persist:x32