In the face of Heavenly-rank, Earthly-rank, and even lower spiritual weapons, such issues are not fatal.

Because even with a Heavenly-rank spiritual weapon, a skilled weapon refiner can find a way to reshape the artifact spirit.

Or simply dispense with the artifact spirit, letting the warrior act as the spirit, using spiritual energy to control the weapon instead.

This is because spiritual weapons below the Heavenly-rank aren't so complex that a warrior can't fully understand them.