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.
I'm just getting into woodworking. This has been a consistent source of confusion. It's no simpler with rough lumber. The usable yield of 4/4 (i.e. four quarter, or a one inch thick rough piece) is at least 13/16 of an inch after surfacing two sides.
That said, even after building with dimensional lumber for decades, it's still weird to me that a 2x4 isn't 2x4.