The battle between the Homeland Titan and the Meat Mountain Starship was essentially a brawl between two massive monsters bristling with an array of weapons. However, although the Meat Mountain Starship could form massive maws on its surface at will, launching magma light beams of varying power, in essence, it only had this one mode of attack.
Unlike the Elder Race, which easily claimed dominion over the universe, the Pilgrims, while also possessing incredibly powerful technology, could not possibly be as comprehensive as the Elder Race, nor could they match the Elders in utilizing abilities.
Thus, while they possess the ability to modulate the genes of living beings and craft tens of billions of humans and other organisms into the Meat Mountain Starship, even utilizing this "living starship" to extract energy from the core of planets, the Pilgrims lacked the ability to master more complex systems.