The Superflare from Dangerous Covenants, a modified Flare-S, is described as having its handling hampered by the big gun bolted to the thing, yet its handling is unchanged from the regular Flare-S. Is this just a misprint, or an example of gameplay/story segregation?

After reading both profiles, I think it uses the term 'handling' without realising it's a word that carries special weight in regards to vehicle statistics.

That said, the drawbacks seem to be based on using the weapon (Additional Rules > Oversized Weapons) rather than just having it passively impact the maneuverability of the craft.