I don't think they changed his origins, because that in and of itself would also change Shao Kahn's origins and would just be a mess. I just think they're tying the Red Dragon to him. Like the Red Dragon discovered who he was, and then worshiped him. I don't think any of this implies that they created him or that he exists because of them.
Well, let's wait. Because, for me, just by the fact that they added Onaga on Red Dragon lore...eek.
The game (Kenshi's ending) works exactly with Armageddon's plot (when it comes to Taven/Daegon), even if they consider all of those events suspended/postponed/even cancelled.
IMO, it's a waste to put Outworld's Dragon King with the weak edenian Red Dragon, since their only cross was that Blaze thing.
To tell you the truth, I wouldn't mind if Daegon started looking for Onaga AFTER his original plans. But Goro said Onaga is part of the Red Dragon's lore...and Kittelsen mostly implied he may rewrite his origins.
As said before, let's wait. 99% of chances of me getting mad hahahah (as every expected idea in the comic), but...
I mean, the kamidogu being daggers in this timeline doesn't make sense either, nor does Shinnok's amulet being the genuine article or Mileena not being born until during MK2. It was a soft reboot technically, but they've hard rebooted a lot of stuff.
I think he put daggers because the One Being was split into the realms. I thought it was a clever idea, and the Kamidogu have never been revealed at all what they were. I don't think that's changing everything, he adapted.
About Mileena, well, NRS did that, not a third part. The original creators have their means to adapt, but someone that clearly had no exact contact with the source material and commited several mistakes...that's worrying.
What do you mean about the Amulet being genuine article? You mean the main object of the plot? Once again, the game is the voice of the creators, they know how to fit most things. Another thing I thought as clever, since the Amulet is one of the (if not the most important) object in MK lore, remembering it was center of many games (MKM:SZ- MK4, MKA-MK and MKX), probably having an important role in MK11 (Raiden).