If you're going to balance the rotating assembly, then you need to balance the whole rotating assembly.
In an ideal build, you balance the pistons so that they are all the same weight, you balance the rods so that they are all the same and the piston/rod combos are the same. Then you balance the crank with the assumption that the identical piston/rod combo is hanging off of each.
There is no way that you would go to the effort of balancing the crank to suit unmatched piston/rod combos.
By the same token, the are any number of engines that have been slung back together with completely unmatched/unbalanced parts. It's all a matter of what you want to achieve. Bazzilion revs? Balance it. Minimise losses? Balance it? Drive it to the shops below 4000rpm 99% of the time? Save some money (by not spending as much on balancing).