+1. A square taper bottom bracket and crank only go together at 90° increments so getting the crankarms aligned properly is pretty trivial and any set of opposing flats can be used.

Octalink and ISIS bottom brackets offer more chances for misalignment so you have to be sure the arms are installed 180° apart, not just close. Again, you can start with any spline arrangement on one side and use the appropriate ones on the other side.

A Shimano Hollowtech II crank has the drive side fixed to the spindle and the non-drive side arm is keyed to the splined spindle end and will only go on one way.