Data clouds from 3D laser scanners can be resolved into curves that represent the tank shell at any elevation. Mathematically constructing a best fit circle from this curve gets you a tank center. Evaluating roundness is now straightforward for that elevation.
The same can be done for the entire tank - a best fit cylinder can be created from the data from which lean, deviation and roundness can be derived.
There are many ways to slice the data - another is to create a best fit curve, circle and cylinder from the lowest 12" of the tank, and evaluate lean, deviation and roundness from those.
For example, API 650 measures roundness at 3 feet above the bottom and has roundness tolerances that vary with tank diameter, allowing greater variations in larger tanks. For this example, roundness from a data cloud as described above is a fairly straightforward exercise.
The OP's question was more of "where did this tolerance come from?" My guess is that it is a way to insure quality construction and suitability for service rather than some structural requirement or FEA analysis. Sometimes an organization just picks a number out of thin air and over time either adjusts or sticks with it noticing that it "works", and thinks no more about it.