Constitutional issues always trump precedent. Happens all the time. E.g. Heller v. D.C.
Then please explain Raich, wherein non-commerce was considered within the purview of Congress's "commerce clause" with the 'extension' of the "necessary and proper" clause.
Please explain Kelo, where imagining numbers from private redevelopment is considered filling the "public use".
Please explain how a "right to privacy" applies between patient and doctor to allow the striking down of state abortion laws — but doesn't apply in the case of the government domestically spying on its citizens (NSA), or even between patient and doctor in general (electronic medical record requirements of the ACA).
The fact of the legal matter is that the Supreme Court can pull whatever it wants out of its ass — see the ACA ruling, for example.
The rest of the Judiciary does the same: they build up their case to support what they've decided beforehand.