If Vehicon factories can be as easily destroyed as seen in this episode, how come the Maximals never targeted them before?
Optimus Primal reasons that the captured Transformer Sparks cannot be released because he fears Megatron would recapture them. This is a crucial logical mistake on his part. By releasing the Sparks and placing them inside new bodies, he would gain a large number of allies, troops with which to fight the already weakened Megatron. Not to mention, if Megatron captured them again, it wouldn't be too difficult to find and release them again either. But instead, he leaves the Sparks where they are and continues to rely on his few friends to win the war.
Megatron's small and frail Diagnostic Drone body manages to survive an immense explosion at ground zero. Considering the explosion tore the factory apart, it should have detonated him as well.