reuse Cyclone IV fpga Pasive serial configuration pin for SPI
These settings take effect AFTER configuration completes.  So they will behave as configuration pins while the FPGA is being configured, then control will be turned over to your design after configuration is complete.  I presume if you reset the whole FPGA back to an unconfigured state, the pins will revert back to configuration pins to reload the design.  IOW, this should work fine and allow you to use the pins in your design to access the configuration SPI bus.