Re: Clarence Thomas's concurrence. There is disagreement on the Right about the substantive due process (SDP) doctrine. This is the idea that the due process clauses of the 5th and 14th Amendments protect unenumerated, so-called "fundamental" rights. (There is pretty much no debate about it on the Left. They love SDP, because it's a massive source of judicial power they can wield to get their way when they lose in the political branches.) Some on the Right are OK with SDP in principle but think liberal courts have misused it - meaning they've said that many of the rights they've assumed into law aren't really fundamental. Some, like Don Willett would also like to use SDP to impose a laissez-faire economic policy, such as reviving the Lochner Doctrine that struck down minimum wage laws.
Others on the Right (like Thomas, Bork, and myself) think the entire doctrine is wrong. First, not only is it not in the Constitution, the very concept of substantive due process is an oxymoron. It is the opposite of what the law actually says, and let's remember what a court is. It is supposed to apply laws (especially acts of Congress, including the Constitution) to facts. Well, if it's acting without a law to support its actions and definitely when it's acting in opposition to the written law (as every SDP case is), its actions are wholly illegitimate and an abuse of judicial power.
Second, though the SDP doctrine has come up with certain criteria it considers to determine if a right is "fundamental," all of those criterion are subjective and can be spun in any direction. In practice, a right is deemed "fundamental" if the Court is sympathetic to it, and it is not deemed fundamental if the Court isn't sympathetic to it. It's nothing more than an exercise of raw and lawless judicial power regardless of who is doing it and to what end.
Here's where it gets really dicey. SDP is the legal mechanism by which the substantive rights in the Bill of Rights (like freedom of speech, religion, etc.) get applied to the states. If you dump it, most of the gun rights cases go. The religious liberty cases also go. A state could theoretically declare an official religion, have taxpayer funded churches, etc. unless they were prohibited by state law. (The procedural rights like right to a trial by jury, right to counsel, etc. would not be affected.)
Though Justice Thomas rejects the entire doctrine, the rest of the Court (including the other conservative justices) do not. Otherwise, they would have joined his opinion instead of Alito's. I'm not sure why gay marriage would necessarily have to go. Though Obergfell relied in part on SDP, it also relied on the equal protection clause. That means you could dump SDP and keep gay marriage. Same for interracial marriage. So is gay marriage really in jeopardy? No. Even if Thomas wanted to dump it, he's one vote. The rest were very clear that they weren't going to do that.
Re: the justices calling Roe "settled law." They weren't disingenuous. When they were answering, they were doing so based on the circumstances at that time. It was settled law. Something can be settled and still be overturned. See Plessy v. Ferguson, which was very much settled law - until it wasn't. They never promised not to overturn it. During their confirmation hearings, Earl Warren and William Brennan would have said the same thing about Plessy.
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