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The Court emphasized in both cases the actual operation of the agencies, the powers they wield. It was core to the ruling and shows the difference between the cases.
The FTC wields inherently governmental, executive power. It can levy fines, participate in federal rulemaking, budget out of the Treasury, etc. In short, it can use the might of the state against you, to use strong language.
The Fed, overall, doesn't really do that. When it issues interest rate targets or floats its own bonds it isn't using the police to set its policies.
One executes US law, the other moves around its own money. And because the one executes US law it is executive, and executive power rests in the president constitutionally.
Make sense?
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