As long as the lumber is a standard size then it can be accounted for. The problem is that when dimensions get too far from what you need then you have to use more lumber and/or make a lot more scrap, leading to more cost in both material and labor. A lot of things in home building are based upon standard lumber dimensions.

That said, even after building with dimensional lumber for decades, it's still weird to me that a 2x4 isn't 2x4.