The break-even works out to "small ships use small guns, big ships use big guns", more or less. Consider the following:
20x NAC/40 = 800 capital damage, 90,000 tons weapons, no fire control = 90,000 tons total.
vs
160x Medium Sub-Cap cannon = 800 capital damage, 80,000 tons weapons, 64,000 tons fire control = 144,000 tons total.
But yes, it does say bad things about medium-sized ships (that don't saturate their fire control) using full-size guns. Which is a bit silly, but the rules are a bit wonky in places, and this is one of those places.