the level 7 has the brains to know what's going on and said that all the humans on the planet should die, if it doesn't take out the transport part of the humans can escape.
The centipede wants to kill all humans. If they can’t leave the planet they’re trapped and can be killed off completely. So destroying the transport makes sense. And you have to remember that it absorbed the Magus, so it has his memories to use. 🤔