The really fucked up thing about it is, the Appointments Clause is concerned with Separation of Powers, that is, the extent to which Congress can impose limits (or expand) the authority of the Executive to do things, such as appoint superior officers without the advise and consent of the Senate.
That is what most of this litigation in the past has centered upon.
But this regime of appointing special counsel has nothing whatsoever to do with Congress: it occurs entirely within the Executive branch. By regulation, the SC can only be removed for cause by the AG. But, presumably, given that the AG reports to the President, the AG could be ordered to remove the SC.
She fucked the dog on this. BIg time bro.
If SCOTUS followed her ruling, they would be taking power away from the Executive, which is something they're not particularly inclined to do. Unless it gives power to them, which this would not.