Grav wells do more damage the closer to the event horizon your ship is. Grav wells spawn with the transformers right in the middle. It dies make sense why some do it. A shame they don't throw ut on the spheres though
If you time it correctly, you pull the 2 spheres that warp in down to the level of the transformer. Means you take out the transformer and then the spheres without have to reposition and before the spheres split up. Or at least it used to work until they got their EPtE buff.