THe FTC is part of the Federal Gov't whereas the Federal Reserve is not.
The Federal Reserve System is a bit more complicated than the Board of Governors (but is also effectively part of the federal government, but a sui generis, highly corporatist part of the federal government, with direct involvement in an unusual manner by powerful private entities.)
I think you know that blanket statements of this type are at best inaccurate and not helpful to the discussion. The Fed is an entity created by federal statute and staffed by presidential appointees, so it's at least a little misleading to say that it's not part of the federal government.
The Court will have a bunch of briefs from both sides giving them legal justification for any decision. They will choose which briefs they like.