Several comments:
Dots on tires: There is no standard way of doing this. Some tire manufacturers use the dots, some use something else, some don't mark at all. Further, there is no standard that wheels have to be measured and marked - and many wheel manufacturers don't use the valve hole as the mark.
Then there is the issue of what the dots mean. It is common for the red marks to be used to indicate the tire's uniformity high point (think runout and you'll be close) and the yellow dots to mean the heavy spot of the tire (balance), but this is far from universal. The idea is to match the high point of the tire with the low point of the wheel to get a "rounder" assembly. This is NOT the same as minimizing the balance weights.
Please note, it is possible to have a perfectly balanced, but out of round, tire and wheel assembly.
And lastly, it is quite possible to have a tire not get fully seated on the wheel. For some reason, most tire mounters don't realize that a bit of lube on the beads AND the wheels helps the tire fully seat. Some runout issues can be traced to this.