The Supreme Court vs a San Francisco Judge: who decides

I heard this news and I should probably spend more than 2 minutes trying to figure out what is going on but this is my understanding:

The Supreme Court on Friday, May 30, voted 7-2 to stay a Massachusetts court order (signed by Judge Indira Talwani) which prohibited the US government from deporting some 500,000 immigrants who had temporary permission to live and work in the US.  The decision is 24A1079 Noem v. Doe .  Two justices dissented, Jackson and Sotomayor and most of the written decision is their dissents. (The appellate court is still reviewing the judge's orders other than the preliminary injunction, and the Supreme Court anticipates hearing the case through certiorari later).   

The news media reported that this decision allowed the Trump Administration to end parole for 500,000 immigrants and start deporting them.  See: https://www.youtube.com/watch?v=-2hE3Y_8kQg ("Supreme Court allows Trump to end parole program for 500,000 immigrants").  This may be correct - it seems that DHS can deport these people while the appellate process is pending until the Supreme Court either declines certiorari or until they make a full ruling on the case agreeing with the judge.

So this decision was released on Friday, but it is unclear what time, probably before noon.  AFTER this decision was released, but also on Friday, a judge from San Francisco, Edward Chen, ruled that his injunction, separate from the Massachusetts one, was not affected by the Supreme Court decision on Friday.  Edward Chen's injunction had been overruled by the Supreme Court in a different case, 24A1059 Noem vs National TPS Alliance on May 19, which was very similar to the Noem v Doe order, except only Judge Jackson dissented, not Judge Sotomayor.  The Northern California case is No. 3:25-cv-1766.  (I don't understand how this case differs from the Massachusetts one because they both involve TPS protection for Venezuelans).  This is Chen's original order: https://www.aclusocal.org/sites/default/files/2025.03.31_93_order_granting_postponement_motion.pdf

In any event, Judge Chen's injunction was directly stayed by the Supreme Court on May 19, and Judge Talwani's injunction was directly stayed on May 30, but Judge Chen says that his injunction can continue.  His reasoning? 

The justices provided no rationale, which is common in emergency appeals. But they singled out applicants who had received work authorization and other paperwork with new expiration dates of Oct. 2, 2026.  Chen said at a hearing Friday that the justices could have stayed silent as to that subset of people, but didn't. His court continues to hear the underlying claim that the revocations by Homeland Security Secretary Kristi Noem were unlawful. https://www.yahoo.com/news/judge-blocks-administration-revoking-protected-192726356.html  

So Judge's Chen new order only helps about 5,000 Venezuelans who have Temporary Protected Status that expires exactly on October 2, 2026.  But is he disobeying the Supreme Court, or did he find a loophole in their decision?  I have no idea, this is very confusing.  It seems that he is choosing to disobey the Supreme Court order.  I don't know the answer, I am just pointing out the problem.