Typically I keep the engineer on the gat still firing greased, the magazine dumps faster and during reloads they just turn around and wack the balloon with the mallet.
The gat is also less effective with different ammo types, at various ranges, good for specific strategies like using heavy clip to disable, incindiary for annoying engines and charged for faster armor stripping.
But the chain gun strips armor usually before it's clip is ever spent, so I'd rather have the gunner on flak with multiple ammo types so they can take full advantage of an armor less ship in the distance, or close range, using charged, les or heavy clip as needed.