Yes, in fact, it's more often called shiny-swapping because shinyhunting is what it's mainly used for, but it can also be used for natures and, to an extent, IVs. Although keep in mind that if you save after the day care finds the shiny egg, you can't swap onto another Pokemon. Also, you can't go from Masuda Method to non-Masuda (I'm 99% sure you can go from non-MM to MM, though).