Yes, it is safe to ignore incomplete I/O assignment warning messages in the Quartus® II software, for dual purpose configuration pins that are used for Active Parallel (AP) configuration.
The current strength and slew rate assignments on these AP configuration pins should be left to default, but this will result in the generation of incomplete I/O assignment warning messages by the Quartus II software related to missing drive strength and slew rate assignments.
To prevent the warning messages being generated, use the following QSF assignment for the appropriate pins :
set_instance_assignment -name <parameter> DEFAULT -to <pin_name>
set_instance_assignment -name CURRENT_STRENGTH_NEW DEFAULT -to flash_data