Exactly. He is upholding the general principle of stare decisis, but that doesn't mean that a prior SCOTUS ruling cannot be overturned. It has been done repeatedly throughout our history.
Dred Scott was a SCOTUS decision.
Plessy v Ferguson was a SCOTUS decision.
The Court can be wrong. Bad decisions by the Court ought to be overturned. The Liberals would be the first to agree with that (they like Brown v Bd of Education a lot better than Plessy).
Roberts supports stare decisis, as he should. But he is not bound by past decisions (and he knows it).
It might be a good idea to demand Republicans keep their promises and nominated a verifiable orginalist in the future and hold them accountable if they don't at the ballot box.