1. There are problems with this. One, Argus is a god and Rain is only 10,000 years old. Rain was only a child when Shao Kahn conquered Edenia. So that would mean Argus and Rain's mother would have had to given birth to him right around the time the 10th MK tournament for Edenia and Outworld, which is highly doubt. Argus is the Protector of Edenia, so I would think he'd be more concerned about the safety of Edenia than getting laid. So unless NRS ever reveals otherwise, the Edenian general IS the biological father of Rain. It would make much more sense.
2. So a cameo automatically confirms Daegon is making future appearences? Um I don't think so.
3. This is factually incorrect; they HAVE changed more than the paths of the timeline, more than once. Look at the backstory for Mileena. She was created during MK2 in the new timeline, and Shao Kahn favors her over Mileena. In the original, he favored Kitana and created Mileena in case Kitana ever found out the truth about her past. Also, Ermac was revealed in MK9 to be an entity of Edenian souls. In UMK3, he was said to be comprised of Outworld souls. In the original timeline, Kabal became a cop after the events of MK3. In the new timeline, he was already a cop before the events of MK3.