With any cotter pin you should expect to do some filing of the ramp on the cotter to achieve the correct angle of 180 degrees apart of the crank arms.
I don't think it's so much the "phasing" of the crank arms as it is to get an accurate tapered fitment along with proper installation. Unless there's even contact across the taper there'll be some yielding and creep that leads to wear and looseness. I found this out the hard way with my 1st cottered crank and daily use many moons ago.