Just a theory. The difference in size of the coins may have been important in the shape of the flan. These coins were produced by cutting slices from a roll of copper, much like a sausage.
To check my theory, you can experiment with a roll of dough. It is relatively easy to roll the dough in a thick sausage shape with your hands. Start with a ball and roll with appropriate pressure.
The thinner the sausage becomes, the more important it is to exert the right pressure, to have a smooth working plane and not to have an lumps in the dough, even to have sausages that are not too long. Any of these will cause deformations in the roundness of the sausage, making it look more squarish. Further inexpert rolling the sausage will tend to reinforce the squarishness of the sausage. In this way, with a material that is thicker and much more difficult to handle than dough, slices of thicker sausages would tend to be more round.
Peter