Terrible reading... and watching.... comprehension.
We have proof the other Kryptonians didn't have powers. If they did, Lois couldn't have kicked one off or killed several with a mere handgun. Only those Kryptonians allowed into the field had powers, because they had breathed Earth's atmosphere (Jax-Ur says as much to Kal-El, "The strength you derive from Earth's Sun has be neutralized aboard our ship. Here, in this environment, you're as weak as a human." Ridiculous to say if all the Kryptonians were powered on the ship.)
Zod was not OK with every Kryptonian having powers. If he was, there was no need to terraform Earth or use the World Engine. He could have ferried Kryptonians to Earth and let them conquer and destroy that way.
He didn't do that.
Rather, he allowed about three Kryptonians to be in the field, then, after asking whether Kal-El needed to be alive to retrieve the Codex, set in motion the World Engine... the clear implication being that the World Engine may or might kill Kal-El because he would have been powerless, just like all the other Kryptonians would be on a terraformed environment, just like all the Kryptonians were on the ship with Kryptonian atmospherics.