Salaamun alaikum,
Nice link ... the science is solid, very well done! Some of my understanding/leaning on your observations ....
1. In 67:5, 41:12, God says the "lowest sky" or "the sky of this world" (السَّمَاءَ الدُّنْيَا) was adorned with lamps, which have to be stars. In 10:5, 71:16 the sun is described with other synonyms of lamps. In 37:6 كَوَاكِبِ can still mean planets, since they orbit stars. Which means God adorned the lowest sky with planetary systems.
- note: stars and planets did not adorn our universe when God created it. Stars adorned our universe later (estimated as a couple of hundred million years after the creation).
2. Just like الْحَيَوةَ الدُّنْيَا - "the life of this world" which is life in our universe, I understand السَّمَاءَ الدُّنْيَا as the sky that we can observe from this world - i.e., our observable universe, so I agree with your "third scenario". 41:12 says each sky was given its own law (أَمْرَ). So the laws that govern the other skies may not be the same as in ours.
3. 65:12 can also mean similarity in number. I.e., every sky also has land (الْأَرْضِ) in them.
Peace.