So I read the article and if you look at the paragraph that starts "Under the Fourth Amendment..." and then look at the underlying case law it seems the checkpoints we go through on the way to Rocky Point meet the Supreme Court ruling.
The immigration check points returning from Rocky Point seem to be legal. They are within 100 miles of the border with a nexus to a border crossing spot, and the stop consists of only a couple of questions. The only issue, per case law would be if they used drug sniffing dogs as probable cause for a search of the vehicle. The ruling also came from a New Hampshire court, so I would question any application to Arizona. If a federal court were to make a similar ruling, it may apply.