It's NOT an issue. Think about it like this. How many 2 blade broadheads are on the market. Obviously you can't line up 2 blades with three feathers[8D]OR, how about the 4 bladed broadheads, you can't line them up with three feathers either. If it were an issue, do you think these broadheads would be ever used.
Why not try to line the broadhead with your fletchings on one of your arrows, and then do the opposite with another arrow, shoot them both. I'll bet they fly the same. If not, you've got a tuning issue and no matter the alignment, you've got other issues!