Several points.
First: The case you seem to be referring to (which took verifying the quotes to be certain of, because of a few errors you made) is Edmond v. United States, 520 US 651 (1997), addressing the appointment of judges to the Coast Guard Court of Criminal Appeals, and the decision of the court was written by Scalia, J., not Rehnquist, C.J.
Second: Given the fact that the judges of the FISC (and the FISCR) are already judges appointed to other Article III courts by advice and consent (just as was the case with the Emergecy Court of Appeals and the Temporary Emergency Court of Appeals), Edmond, by reference to Weiss, illustrates why it may be unnecessary to inquire as to which appointment procedure under the Appointments Clause is necessary (whether they are "principal" or "inferior" officers), since the members of the court are already appointed under the Appointments Clause before being assigned to the FISC or FISCR:
(Edmond, at 654): In Weiss v. United States, 510 U. S. 163 (1994), we considered whether the assignment of commissioned military officers to serve as military judges without reappointment under the Appointments Clause was constitutional. We held that military trial and appellate judges are officers of the United States and must be appointed pursuant to the Appointments Clause. Id., at 170. We upheld the judicial assignments at issue in Weiss because each of the military judges had been previously appointed by the President as a commissioned military officer, and was serving on active duty under that commission at the time he was assigned to a military court. We noted, however, that "allowing civilians to be assigned to Courts of Military Review, without being appointed pursuant to the Appointments Clause, obviously presents a quite different question." Id., at 170, n. 4.
Third: The factors Scalia identified in finding that the members of the Coast Guard Court of Criminal Appeals were inferior officers was not that "the military reports directly to the Secretary of Defense" (as, in any case, the Coast Guard, at the time, reported to the Secretary of Transportation), but rather that oversight of the Coast Guard Court of Criminal Appeals was found in the Judge Advocate General of the Coast Guard, who had certain rulemaking and other administrative authority, and the Court of Appeals for the Armed Forces, which exercises limited review of the decisions of the Coast Guard Court of Criminal Appeals; for the FISC, there is certain (though different than that exervised by the Coast Guard JAG over the Coast Guard court in Edmond) administrative authority vested in the Chief Justice (in part to be exercised in consultation with the Attorney-General and the Director of National Intelligence), and review authority in the FISCR (and, for the FISCR, the same administrative authority, with review authority in the Supreme Court.) However, Scalia also noted that it was important (though not expressly necessary) that this supervision was exercised within the Executive Branch, so application of Edmond to the FISC and FISCR in terms of inferiority seems somewhat murky.