There is less debate about medium guns- those ships (galleon, goldfish, spire) pretty much always have a gunner, because you need projectile speed mods (incendiary/heatsink) to get around arming time restrictions at close range on the heavy flack and lumberjack, while heavy shotguns benefit a lot from switching between lochnagar/incendiary/heavy/charged, in order of usefulness. Hwachas also require a heavy clip at anything but point-blank range, though an engineer can easily just load vanilla rounds at close range with little loss, so they don't lose out as much by not having a gunner. A hwachafish is still fully viable with 3 engineers, but a blenderfish is hurt by not having a gunner.
That being said, most popular ships (ones with no medium guns) really don't need a gunner that much, because enough damage/range versatility is provided simply by being engineer and taking either a close-range (greased or incendiary) or a long-ranged (heavy or lesmok) tool, and then switching to vanilla ammo when the tool becomes less useful. Exceptions include rare weapons such as the artemis which only really benefits from burst, the banshee only really benefits from greased, etc.
Engineers simply bring more to the table, between buffing components (including weapons, giving the benefits of charged rounds), extinguishing, and repairing. In a close-range light-gun ship that's guaranteed to be taking lots of damage, a gunner simply can't keep up with repairs and their fancy ammo types are useless if the rest of the ship is broken.
p.s. we already have an epic thread about this.
https://gunsoficarus.com/community/forum/index.php?topic=410