When this option is enabled for Cyclone® III and Cyclone IV devices, the dual-purpose pins settings are overridden by this option. Therefore this will tri-state the DCLK, nCSO, DATA[0], and DATA[1]/ASDO pins which will prevent the ALTASMI_PARALLEL from working correctly in user mode.
If you require the use of these dual purpose pins in your design, you should keep this option disabled. The Quartus® II software versions 10.0 through 10.1 do not provide a warning or error message to indicate the dual purpose pins will not function per your design requirements when this option is enabled and when using the ALTASMI_PARALLEL megafunction.
This option was introduced in the Quartus II software version 10.0.