Yes you can (unfortunately). Read here: https://itch.io/jam/gbjam-5/topic/40657/how-is-thi...
I would like to have old classic GB hardware but it seems you can pick any colors and swap as much as you want to ( as long as you have 4 c on screen). So basically you could do any kind of palette-rotating effects. I will personally stick with classic 4 grayscales.