Seems Thomas was sending a signal in this ruling to Aileen Cannon on the classified documents case that she should rule that Jack Smith was improperly appointed. This is what Trump's lawyer have argued there.
JUSTICE THOMAS, concurring. Few things would threaten our constitutional order more than criminally prosecuting a former President for his official acts. Fortunately, the Constitution does not permit us to chart such a dangerous course. As the Court forcefully explains, the Framers “deemed an energetic executive essential to . . . the security of liberty,” and our “system of separated powers” accordingly insulates the President from prosecution for his official acts. Ante, at 10, 42 (internal quotation marks omitted). To conclude otherwise would hamstring the vigorous Executive that our Constitution envisions. “While the separation of powers may prevent us from righting every wrong, it does so in order to ensure that we do not lose liberty.” Morrison v. Olson, 487 U. S. 654, 710–711 (1988) (Scalia, J., dissenting). I write separately to highlight another way in which this prosecution may violate our constitutional structure. In this case, the Attorney General purported to appoint a private citizen as Special Counsel to prosecute a former President on behalf of the United States. But, I am not sure that any office for the Special Counsel has been “established by Law,” as the Constitution requires. Art. II, §2, cl. 2. By requiring that Congress create federal offices “by Law,” the Constitution imposes an important check against the President—he cannot create offices at his pleasure. No former President has faced criminal prosecution for his acts while in office in the more than 200 years since the founding of our country. And, that is so despite numerous past Presidents taking actions that many would argue constitute crimes. If this unprecedented prosecution is to proceed, it must be conducted by someone duly authorized to do so by the American people. The lower courts should thus answer these essential questions concerning the Special Counsel’s appointment before proceeding.
Thomas seems to care less that SCOTUS has upheld the legitimacy of Independent and Special Counsels in the past.