The U.S. Department of Justice didn't even exist until 1870, so the definition of a "principal appointee" vs. an "inferior appointee" would have to be governed by the U.S. statutes under which the DOJ was created and expanded over time.
Interestingly, the Deputy Attorney General post (established in 1950) and Associate Attorney General post (established in 1977) were established by executive orders or by directives of the U.S. Attorney General's office, not by statute. So it would seem clear that the statutes governing the U.S. Dept. of Justice give some kind of discretion to the executive branch and its DOJ in these matters.
See too, Morrison v. Olsen
Not that DOJ can’t, in the ordinary conduct of business, perpetrate harassment, bad faith prosecution, and so on. It can and does. The fact that it farmed out the dirty work isn’t the issue. The fact that the work is dirty, is the issue.