I deal with those bunkers by tearing off the roof so the bottom levels are filled with sunlight (the ring of glass in the floors), and digging out the ramp areas and breaking the spawners underneath. The I dig down to the mid level and draw the enemies over to a hole in the wall and kill them, then add torches to the few places still dark and dig out the remaining spawners. Then I dig to the bottom level, dig around the outside breaking the 3 spawners, and then I just leave and wait for them to despawn, it's too dangerous trying to fight them, even through a hole in the wall. I come back later and finish lighting the bottom, grab the loot, and then break and collect every single block of the bunker so there's just a deep hole in the clay when I'm done. =p