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For Mortal Kombat, we already know this game is canon. They've said it happens in a unique (but canon) timeline but it's very clearly a mid-qual set between Mortal Kombat 3 and 4.
Considering the MANY references linking back to it, is it possible Mortal Kombat vs DC Universe is part of the Injustice universe? I assume a few things would have to be noted to happen off-screen. Lex Luthor would need to switch sides between games and become Superman's ally rather than enemy. Kronika would take Joker to the MK1 universe before the events of Injustice start.
You might say that it should be the good universe timeline, but Injustice 2 references MKvsDC and that's set entirely within the regime timeline, so logically the DC world in that should be the main Injustice timeline, probably.