DE1-SoC - Change GPIO Output Voltage

Correct, the voltage is not controlled by settings but rather the I/O supply for that bank so if you need to change the level you either need to change the bank supply or use something like a level shifter. The level granularity is per bank so typically you pick the most common voltage for the bank then use level shifters if you need a different I/O level for a handful of pins on the same bank.

By the way, the I/O are capable of a wide voltage swing on the input side. For example if the bank is 3.0V you can typically feed a 2.5V signal into it and the input will be measured as a 0/1 correctly. I suspect if you look at the schematic for that board you'll see some instances of that since it's a fairly common thing to do. See the "I/O Standard Specification" section of this document: http://www.altera.com/literature/hb/cyclone-v/cv_51002.pdf The Vil and Vih values tell you what threshold the input pins will consider the value to be a 0 or 1 so for 3.0V CMOS you can see a 2.5V input is between the min and max of 1.7-3.6 range to be an active high signal. For output signals you don't have this flexibility but I would look at the datasheet of the device you want to connect, it may have the ability to support a wide voltage swing just like the FPGA.