I understand the purpose of the GEC as it relates to setting the neutral to ground potential for safety, but I do not understand the theories of limiting voltages if a higher voltage was applied to the secondary lines such as lightning or primaries contacting secondaries. Could someone give a clear explanation of how this works?

this is a good Q, what if?.... I would venture to say that a solid GEC with many points to earth would serve to bleed off a heavy fault better. the scenario could, with specifics given as to what primary connecting to what secondary, be expanded on here.