AFAIK crankcase halves have been machined together, so it indeed is critical for crank bearing alignment. Otoh, if you find a good machine shop, that will line bore the timing side bush with the cases assembled and in good alignment with the drive side bearing, you will probably get away with it.
But then there is the question of alignment on the camshaft bushes and the cylinder barrel mating surface(s). For the current prices of good, matched sets, I personally wouldn't take chances there.
Cheers, Markus