Programming HPS pins in Quartus II - Unused HPS Pins

Those settings get buried in an I/O programming file that gets built into the preloader binary. So you shouldn't see source files change as a result of an I/O standard change since that information is in a separate binary file. I was told that binary programming file gets turned into a C array of values while the preloader is generated/build (not sure which but one of those steps does it) but it's literally just a list of values at that point and you won't know which value maps to what. If that file didn't change then it's possible that switching between 3.3V LVTTL to 3.3V LVCMOS has no effect on the programming file and therefore that C array doesn't change either.