One thing they didn't talk about was structural: the court system is split up into X circuits, and each circuit is independent. Normally each circuit uses rulings from other circuits as a basis for its judgements, but circuits are pretty independent from each other. The Supremes weigh in when the circuits conflicted with each other.
The national injunctions issued by the lower court allowed the lowest level court to have more authority than an appeals court. An appellate court's decision was only binding on its circuit. Why would a lower court have more authority than an appeals court? That makes no sense.
That's outside of all the reasoning the court used to stop this practice.
That said, if an affected individual brought a suit the may be able to get an injunction, since the court ruled that universal injunctions were inappropriate.