What determines the size modifier (which in turn determines how many points you receive) is shown in the chart below, the number of turns and the number of units (size of file in KB) dictates the size modifier number.
Because the scenario you played fell into the 21 to 50 turns line then the maximum size modifier is 4 regardless of the file size.
As Rick says this table has determined the size modifier for the last 27 years and the logic behind it predates my time at the club, so like Rick I cannot cast any light onto the decisions that lay behind its creation.