Hi, Rajtantajtan
Based on my understanding, the voltage setting should be functioning for all pins except EMI pins, no matter what mux mode you set for this pin. As we can see that for SDHC or SPI, we set pins' voltage to 3V3. So you can do some measurement to confirm it, this is only my understanding, the pin's voltage setting is not just for GPIO. But for some modules that can NOT work at 3V3, we should be careful. The reset value of the pin already make it work at proper voltage, some pins are 1.8V, some are 3.3V, so before you change it, please make sure the devices connected in these pins can work at 3V3.
To change a mux, please modify below file: arch/arm/mach-mx28/mx28evk_pins.c the structure in this file will set the pin's mux and voltage and drive strength etc.. Such as SPI:
1077 {
1078 .name = "SSP2 MOSI",
1079 .id = PINID_SSP2_MOSI,
1080 .fun = PIN_FUN1,
1081 .strength = PAD_4MA,
1082 .voltage = PAD_3_3V,
1083 .drive = 1,
1084 },