I think you may be looking a bit too far into this.In my view this is the central evidence that the entire game is a simulation, along with:
- Oleg gets an area code from a phonecall from space.
- Oleg is basically a mental and physical superman and yet wasn't abducted.
- Kinzie just conveniently finds a ship fully stocked with food, beer and supplies from Earth. Even if we said Zinyak had every ship go out and loot our beer and stuffed sharks, why take our primitive computers?
- If you die outside the simulation, you get the exact same screen shutdown effect you get from within it.
- Weapons, mech suits and power armor are conveniently found outside the simulation when needed.
- The Iron Saint has access to exactly the same superpowers from the simulation, even if we grant that it can fly, why the elemental powers or telekinesis?
- Zin portal spawners appear outside the simulation during the fight with Zinyak
- Anything taken over by the Saints in outside the simulation including the entire Zin empire turns blue immediately, just as it does within the simulation.
Earth is fine. Oleg is fine. The Boss and co are trapped in a simulation within a simulation masterminded by STAG or Dex or somebody.
I don't care if I'm proven wrong later on, this is my headcanon and I'm sticking to it. :3
Don't get me wrong, I would love if they pulled the 'Surprise, Earth never exploded!' card somehow, but most of the points you made just seem like oversights by Volition. I guess we'll just have to wait for DLC/SR5.