There is the multiverse, yes, but the dialogue during battles makes it clear that these fights are still clearly set in the
Injustice universe, even if they're not necessarily canon to the storyline of the series. I suppose the MK universe might have interacted with a completely different DC universe, and Sub-Zero and Raiden simply assumed that the DC characters were the same ones they met back then,* but that's kind of boring, isn't it?
*Possibly backing this up is the fact that the DC characters don't give much indication that they know or remember the MK characters, but we have to bear in mind that a voice actor strike meant that almost all of the core characters' dialogue during their battles with the DLC characters was simply recycled from the core game. It's honestly one of my biggest gripes with the game, because the banter between the core characters had been so great.
...
https://www.supermanhomepage.com/images/man-of-steel-movie10/Skipped/MOS-Excerpt.pdfThis is a behind-the-scenes booklet for MoS, where the most interesting part for me was the introduction that Snyder wrote, and especially the first paragraph:
The single point at which everything we know and everything we question exists in one place; the ultimate crossroads in the journey of discovering the true meaning of ‘self;’ the collision point of science and religion, tangible and ethereal, physical and philosophical; the place where a question that may never truly have an answer can be embodied in a singular character – in many ways, that is the why of Superman.
That's one way to make a bad movie - treat your main character as an idea rather than a person. The rest of the introduction continues in this vein, repeatedly likening Superman to a god, talking about how he'd impact the world, how he'd challenge our perceptions, blah blah blah. What's Superman like as a character, Zack? His personality? His worldview? His motivations?
https://io9.gizmodo.com/justice-league-is-officially-the-lowest-grossing-dc-uni-1823902130lol