As a whole, the pre-balanced cranks will work sufficiently for most of the 47-49mm pistons and the weight difference between the slightly larger piston won't likely be enough to have a huge impact on the balance factor and will work sufficiently.
The real fun would be to not only lighten the pin side of the crank, but actually add weight to the opposite side by drilling and pressing in tungsten weights. For larger bores (52mm or more) it would be the safest and most practical way to achieve a BF higher than 50%.
There are other ways to adjust balance factor without machining the crank counter weights. I wouldn't suggest them without a "do at your own risk" disclaimer though. That means removing weight from the piston side of things. I have seen people do some crazy stuff in the quest for balance work (I have done it too) - up to and including boring the center of the wrist pin out larger (that was the me thnig), matrix grinding the underside of the piston crown (cutting criss-cross patterns) all for the sake of a couple grams. Not recommended for reliability sake, although it could potentially last.