In theory, stare decisis applies the Supreme Court as well (PDF):

“Although adherence to precedent is not rigidly required in constitutional cases, any departure from the doctrine of stare decisis demands special justification.”10

“Special justification” can be one or more of several different considerations, and how strong a justification the Court requires can vary with the importance of the precedent as well as with the importance the Court attaches to overruling it. The decision whether to adhere to a constitutional decision “is a complex and difficult one . . . that must account for a variety of often competing considerations.”11 In reexamining a constitutional precedent, the Court looks to “a series of prudential and pragmatic considerations designed to test the consistency of overruling a prior decision with the ideal of the rule of law, and to gauge the respective costs of reaffirming and overruling a prior case.”12 The Court has looked to the following general considerations in overruling precedent.

[We] may ask whether the rule has proven to be intolerable simply in defying practical workability, Swift & Co. v. Wickham, 382 U.S. 111, 116 (1965); whether the rule is subject to the kind of reliance that would lend a special hardship to the consequences of overruling and add inequity to the cost of repudiation, e.g., United States v. Title Ins. & Trust Co., 265 U.S. 472, 486 (1924); whether related principles of law have so far developed as to have left the old rule no more than a remnant of abandoned doctrine, see Patterson v. McLean Credit Union, 491 U.S. 164, 173-174 (1989); or whether facts have so changed, or come to be seen so differently, as to have robbed the old rule of significant application or justification, e.g., Burnet, supra, at 412 (Brandeis, J. dissenting).13

The silent overrule is the preferred method of the Roberts Supreme Court. That said, ruling the Affordable Care Act unconstitutional without overruling precedents looks like it will be a heavy lift for the Roberts Court. And I am not at all sure they would even want to do it.

Time will tell.

Speaking for me only