The most annoying aspect of the puppet's healing properties wasn't in its fixing speed. The main issue was that the golden flames relied on a source of energy that didn't have clear limits.
The golden halo capable of healing formations used "Breath" to replace and fix inscriptions, but the puppets had only one fuel. They consumed the blood of the Elbas Bloodline to activate their flames and obtain those annoying abilities.
That made the battle more troublesome. Noah and the others couldn't aim to slowly exhaust the reserves of energy connected to the puppets in that situation. They didn't know how their fuel behaved.
It would have been different if the Hive still had access to the Copying Technique. The damage that the leaders could inflict with that asset would be enough to make even those powerful puppets struggle.