the RADIUS overall can effect flash sizes
Are you sure about that? From my experience the radius only modifies the 'size' of the subsystem on the ship. In other words, how far from the given X, Y, Z point that system can still receive damage. Perhaps that modifies the flash size too, but I've never noticed that.
By the way moed, if this is true and you reduce the radius value it will also mean that your weapon subsystem will be harder to hit with weapons fire as well.