config pins and 1.2V

The most serious restriction regarding VCCIO of config pins is the requirement to provide a sufficient voltage to drive the AS memory chip. If you use original Altera devices, it's restricted to 3.3V. On input, a lower voltage IO standard can be overdriven without problems. The JTAG interface can use different IO standards, USB Blaster e.g. allows any IO standard down to 1.2V. DEV_CLRn is rarely used as a dedicated pin, I think.