Commerce Clause allows Congress to preempt state law when acting within it's bounds, sure. Executive agencies (including “independent” ones) don't have that power except through Congress exercising its own preemptive power, which this court does not find Congress did in a way which covers this particular FCC action.
This is more related to federal law preemption. The federal agency gave up powers to regulate. Similar to the betting regulation that has been overturned, allowing states to regulate betting.