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Reimos: Different World, Different Mechanic/Physic.
We have tons of series already which showcase that
Magically Power Scientific Weaponry is more powerful than just either Scientific Weapon or Magical Power separately.
We have already seen the power of that broken Ship in Chapter 045.
Just one shell was enough to destroy half a mountain, that to a randomly fired not properly managed shot. If the functioning and power output is fixed, then it could easily bypass Grain's defenses.
Plus we don't know that Ship's Defensive Powers after being subjected to the Mechanic/Physic of a Different World. Its entirely possible that the Ship might be able to Negate any type of Magical damage.