They don't need to be in line with the fletch, but I do believe in making them all the same. I line them up so that when I lay an arrow on a flat surface like a table, the 2 hen feathers touch and so do 2 of the blades.
Not that they spend much time laying around, but I wanted them all the same, and that was the best reason I could find to choose one orientation over others.

I'm shooting aluminums, so after I get the BH tightened, I just warm up the hot melt for the insert again and rotate the head with a BH wrench until they are lined up. When making up carbons whose inserts are glued in, I'm told that there are washers you can put behind the BH to change the alignment.