Our ability to measure uniformity and imbalance far exceeds our ability to manufacture uniform and balanced tires. A great amount of improvement has been made, but the manufacturing of tires is so complex, there are a lot of opportunities for non-uniformity and imbalance to enter.
And one other comment: There is no consistency between tire manufacturers as to what the dots mean - or even if the dots are there or not!
Further, wheel manufacturers don't routinely mark their wheels. The OEM's do specify the wheels and tires have to be marked for uniformity, but each OEM requires different marks and wheels are typically marked with a removeable sticker.