I think that in general, if you are going to make your color scheme different for recognition reasons you might as well replace the least contrasting color with the most contrasting color. In bad lighting or when I'm turning fast, yellow can blend in with green and/or white. Having black and white makes more sense to me on nxn puzzles since they contrast with any other color extremely well, but on megaminx I replaced white with black since having that tan color looks way too similar to white. Now if that tan was closer to yellow, then I would switch black with white, and then black with yellow. Square-1 is different from other nxns since the U and D faces are the only ones that share colors, so having more contrast with that just helps a little bit with "tuning out" the D layer pieces. With nxn puzzles, its a good choice to use black since it has by far the most contrast out of any other color you could pick, maybe aside from white.
Overall, if you are going to change colors, make the most out of it.