An intriguing aspect of West Virginia State Board of Education v. Barnette involves the Justices' choice of partners in making the sale to the American public that the Constitution embodies a more robust right of individual conscience than what they believed a few years earlier. The background assumption many scholars work with today is that, all things being equal, the Supreme Court prefers not to go it alone, particularly when the institution anticipates controversy ahead. Robert Jackson's early drafts of the opinion suggest that his preferred partner originally was the presidency. This makes sense on a number of levels, given that executive branch officials had flooded the zone on the matter, Jackson and others may have honestly been swayed by their statements and actions, and independent reasons exist for thinking that the modern presidency enjoys an influential role in framing constitutional questions.
But Jackson at some point appears to have changed his mind during the opinion writing process, and the published opinion not only sought to erase the appearance of presidential cooperation but also gestured toward Congress. Sandwiched between two sentences in Barnette on the risks to the Constitution posed by overzealous local officials is this sentence: "The action of Congress in making flag observance voluntary and respecting the conscience of the objector in a matter so vital as raising the Army contrasts sharply with these local regulations in matters relatively trivial to the welfare of the nation."
Note that the argument is only that the passage of a recent federal law and the existence of a textual commitment to Congress "contrast sharply" with a relatively minor claim by local officials to work in the federal interest, not that the federal law or Congress's power to raise an army is actually violated by a mandatory flag salute. In other words, a clash of federal and state interests is a strong suggestion rather than a firm conclusion.
What caused this aspect of the switch and what does it reveal?
The decision to swap partners merits further digging and rumination. For now, let me offer a few additional thoughts beyond my prior writings. First, the development may reflect no more than respect for formalism, since the administration was not a party to the action. On the other hand, DOJ was not present to defend the flag law or Congress's power to raise an army, either, so while formalism may explain in part a decision to jilt the presidency, it doesn't completely explain the Court's decision to take up with Congress. The argument that the federal flag law preempted conflicting state and local laws was made in the DOJ lawyers' article, pressed by the ACLU as amicus curiae below, and rejected by the three-judge panel that first heard the action—which means that the Supreme Court ended up watering down the argument, but found it useful anyway to imply federal-state friction. Still, at least the argument had already been made somewhere during the lawsuit.
Second, formalities aside, Congress is often an attractive partner because many Americans think of the legislative branch as most in tune with popular preferences. As an institution, it also has a hard time talking back in a single voice. Given the collective action problems involved in repudiating the Barnette Court's inconclusive assertion of a federal interest in all matters concerning the flag, the Justices may have felt it reasonably safe to imply that the Court and Congress were in accord on the matter. Since it hadn't issued a strong endorsement of Gobitis already, Congress was unlikely to do anything to shatter the illusion of Judiciary-Congress cooperation (though you can never fully predict a reaction to legal decisions).
Third, seeking cover behind legislative prerogatives may reflect some hangover effect from the New Deal years—including increased suspicion of presidential authority left over from the court-packing crisis. It is possible, of course, to argue that FDR was not nearly as popular in the 1940s as he had been in the 1930s. If this is true, then the contingent, oscillating nature of a particular office-holder's popularity may have affected the ultimate presentation in Barnette.