To my opinion, the device manuals are clear in this point. As they are rather verbose, you may have missed the respective statements. In my own words:
- The output voltage of an I/O bank is exclusively determined by VCCIO.
- VREF pins are used with special I/O standards as SSTL (with DDR-RAM). They only affect the behaviour of the inputs
- assigning a different I/O voltage in Quartus only affects the current strength calculation and is used to check the pin assignment
- interoperation of 1.8V and 2.5V devices may be possibly achieved with VCCIO of 1.8V, if VIH,min of the 2.5V devices can be kept. Otherwise you need a separate I/O bank or level translation.
A
poor mans level translation may be done by resistive dividers for unidirectional outputs