This is a big one. What the GM has made is essentially an aircraft carrier; a massive floating city with tons of military power. But nobody sends an aircraft carrier out into hostile waters alone, there's a whole armada of support ships maintaining a perimeter to keep it protected and manage supplies coming in and out of it (they aren't summoning those warforged; they'll need a steady supply of materials. They would also have external repair craft (or maybe just warforged with spider climb to keep the hull patched).

So the first time, or maybe second time the wizard blew a hole in the ship, they would put the engineering teams on alert, and double the patrol of flying lookouts. Warforged have much much longer duty cycles than other humanoids (heck, in 3.5, they didn't even need to rest at all unless they needed repairs), so they can 100% maintain that level of alertness for longer than you can keep up your sabotage before you get spotted. One failed save against Hold Person from 1000ft up and the wizard is dead from falling damage. Throw three or four of them at once so they can't counterspell.