I am not aware of any requirement that Congress must ratify the FDA's guidelines.
Congress merely needs to “ratify” the FDA’s FoB guidelines by omission—i.e. to not undo them with additional legislation.
As you noted, if the Supreme Court strikes down the Affordable Care Act (a/k/a ObamaCare) in its entirely, Congress would have to reenact legislation to establish the 351(k) regulatory pathway for FoB’s.